diff --git a/dhp-build/dhp-code-style/pom.xml b/dhp-build/dhp-code-style/pom.xml index 77aa2aedb..db0097d64 100644 --- a/dhp-build/dhp-code-style/pom.xml +++ b/dhp-build/dhp-code-style/pom.xml @@ -22,9 +22,20 @@ dnet45-releases https://maven.d4science.org/nexus/content/repositories/dnet45-releases + + DHPSite + ${dhp.site.stage.path}/dhp-build/dhp-code-style + + + + org.apache.maven.wagon + wagon-ssh + 2.10 + + @@ -35,7 +46,7 @@ org.apache.maven.plugins maven-site-plugin - 3.7.1 + 3.9.1 @@ -43,6 +54,7 @@ UTF-8 + sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop \ No newline at end of file diff --git a/dhp-build/dhp-code-style/src/site/site.xml b/dhp-build/dhp-code-style/src/site/site.xml new file mode 100644 index 000000000..634a2c154 --- /dev/null +++ b/dhp-build/dhp-code-style/src/site/site.xml @@ -0,0 +1,21 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-build/pom.xml b/dhp-build/pom.xml index 12b999b9c..97fbdf45b 100644 --- a/dhp-build/pom.xml +++ b/dhp-build/pom.xml @@ -10,6 +10,9 @@ pom This module is a container for the build tools used in dnet-hadoop + + true + dhp-code-style @@ -17,4 +20,12 @@ dhp-build-properties-maven-plugin + + + + DHPSite + ${dhp.site.stage.path}/dhp-build/ + + + diff --git a/dhp-build/src/site/site.xml b/dhp-build/src/site/site.xml new file mode 100644 index 000000000..2d9d769a2 --- /dev/null +++ b/dhp-build/src/site/site.xml @@ -0,0 +1,22 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index c057123b1..7b18f0105 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -13,7 +13,51 @@ dhp-common jar + + + DHPSite + ${dhp.site.stage.path}/dhp-common + + + This module contains common utilities meant to be used across the dnet-hadoop submodules + + + + net.alchim31.maven + scala-maven-plugin + ${net.alchim31.maven.version} + + + scala-compile-first + initialize + + add-source + compile + + + + scala-test-compile + process-test-resources + + testCompile + + + + scala-doc + process-resources + + doc + + + + + ${scala.version} + + + + + diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/application/SparkScalaApplication.scala b/dhp-common/src/main/java/eu/dnetlib/dhp/application/SparkScalaApplication.scala new file mode 100644 index 000000000..6541746b2 --- /dev/null +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/application/SparkScalaApplication.scala @@ -0,0 +1,72 @@ +package eu.dnetlib.dhp.application + +import scala.io.Source + +/** + * This is the main Interface SparkApplication + * where all the Spark Scala class should inherit + * + */ +trait SparkScalaApplication { + /** + * This is the path in the classpath of the json + * describes all the argument needed to run + */ + val propertyPath: String + + /** + * Utility to parse the arguments using the + * property json in the classpath identified from + * the variable propertyPath + * + * @param args the list of arguments + */ + def parseArguments(args: Array[String]): ArgumentApplicationParser = { + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream(propertyPath)).mkString) + parser.parseArgument(args) + parser + } + + /** + * Here all the spark applications runs this method + * where the whole logic of the spark node is defined + */ + def run(): Unit +} + + +import org.apache.spark.SparkConf +import org.apache.spark.sql.SparkSession +import org.slf4j.Logger + +abstract class AbstractScalaApplication (val propertyPath:String, val args:Array[String], log:Logger) extends SparkScalaApplication { + + var parser: ArgumentApplicationParser = null + + var spark:SparkSession = null + + + def initialize():SparkScalaApplication = { + parser = parseArguments(args) + spark = createSparkSession() + this + } + + /** + * Utility for creating a spark session starting from parser + * + * @return a spark Session + */ + private def createSparkSession():SparkSession = { + require(parser!= null) + + val conf:SparkConf = new SparkConf() + val master = parser.get("master") + log.info(s"Creating Spark session: Master: $master") + SparkSession.builder().config(conf) + .appName(getClass.getSimpleName) + .master(master) + .getOrCreate() + } + +} \ No newline at end of file diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java index 0b2cd571f..654fdd5ac 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/HdfsSupport.java @@ -28,7 +28,7 @@ public class HdfsSupport { * @param configuration Configuration of hadoop env */ public static boolean exists(String path, Configuration configuration) { - logger.info("Removing path: {}", path); + logger.info("Checking existence for path: {}", path); return rethrowAsRuntimeException( () -> { Path f = new Path(path); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java index d0909642c..abb9dc148 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/MakeTarArchive.java @@ -85,6 +85,13 @@ public class MakeTarArchive implements Serializable { String p_string = p.toString(); if (!p_string.endsWith("_SUCCESS")) { String name = p_string.substring(p_string.lastIndexOf("/") + 1); + if (name.startsWith("part-") & name.length() > 10) { + String tmp = name.substring(0, 10); + if (name.contains(".")) { + tmp += name.substring(name.indexOf(".")); + } + name = tmp; + } TarArchiveEntry entry = new TarArchiveEntry(dir_name + "/" + name); entry.setSize(fileStatus.getLen()); current_size += fileStatus.getLen(); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java index d8b1cded8..592580ab8 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java @@ -27,8 +27,11 @@ public class GraphCleaningFunctions extends CleaningFunctions { public static final int ORCID_LEN = 19; public static final String CLEANING_REGEX = "(?:\\n|\\r|\\t)"; public static final String INVALID_AUTHOR_REGEX = ".*deactivated.*"; - public static final String TITLE_FILTER_REGEX = "[.*test.*\\W\\d]"; - public static final int TITLE_FILTER_RESIDUAL_LENGTH = 10; + + public static final String TITLE_TEST = "test"; + public static final String TITLE_FILTER_REGEX = String.format("(%s)|\\W|\\d", TITLE_TEST); + + public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5; public static T fixVocabularyNames(T value) { if (value instanceof Datasource) { @@ -195,10 +198,16 @@ public class GraphCleaningFunctions extends CleaningFunctions { final String title = sp .getValue() .toLowerCase(); - final String residual = Unidecode - .decode(title) - .replaceAll(TITLE_FILTER_REGEX, ""); - return residual.length() > TITLE_FILTER_RESIDUAL_LENGTH; + final String decoded = Unidecode.decode(title); + + if (StringUtils.contains(decoded, TITLE_TEST)) { + return decoded + .replaceAll(TITLE_FILTER_REGEX, "") + .length() > TITLE_FILTER_RESIDUAL_LENGTH; + } + return !decoded + .replaceAll("\\W|\\d", "") + .isEmpty(); }) .map(GraphCleaningFunctions::cleanValue) .collect(Collectors.toList())); diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index 6a86f30df..5a59bc0df 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -4,19 +4,19 @@ package eu.dnetlib.dhp.utils; import java.io.*; import java.nio.charset.StandardCharsets; import java.security.MessageDigest; -import java.util.List; -import java.util.Map; -import java.util.Properties; -import java.util.zip.GZIPInputStream; -import java.util.zip.GZIPOutputStream; +import java.util.*; +import java.util.stream.Collectors; -import org.apache.commons.codec.binary.Base64; -import org.apache.commons.codec.binary.Base64OutputStream; import org.apache.commons.codec.binary.Hex; import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.FileSystem; import org.apache.hadoop.fs.Path; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.SaveMode; import org.slf4j.Logger; @@ -26,6 +26,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import com.google.common.collect.Maps; import com.jayway.jsonpath.JsonPath; +import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; import net.minidev.json.JSONArray; import scala.collection.JavaConverters; import scala.collection.Seq; @@ -52,10 +54,56 @@ public class DHPUtils { } } + /** + * Retrieves from the metadata store manager application the list of paths associated with mdstores characterized + * by he given format, layout, interpretation + * @param mdstoreManagerUrl the URL of the mdstore manager service + * @param format the mdstore format + * @param layout the mdstore layout + * @param interpretation the mdstore interpretation + * @param includeEmpty include Empty mdstores + * @return the set of hdfs paths + * @throws IOException in case of HTTP communication issues + */ + public static Set mdstorePaths(final String mdstoreManagerUrl, + final String format, + final String layout, + final String interpretation, + boolean includeEmpty) throws IOException { + final String url = mdstoreManagerUrl + "/mdstores/"; + final ObjectMapper objectMapper = new ObjectMapper(); + + final HttpGet req = new HttpGet(url); + + try (final CloseableHttpClient client = HttpClients.createDefault()) { + try (final CloseableHttpResponse response = client.execute(req)) { + final String json = IOUtils.toString(response.getEntity().getContent()); + final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); + return Arrays + .stream(mdstores) + .filter(md -> md.getFormat().equalsIgnoreCase(format)) + .filter(md -> md.getLayout().equalsIgnoreCase(layout)) + .filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation)) + .filter(md -> StringUtils.isNotBlank(md.getHdfsPath())) + .filter(md -> StringUtils.isNotBlank(md.getCurrentVersion())) + .filter(md -> includeEmpty || md.getSize() > 0) + .map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store") + .collect(Collectors.toSet()); + } + } + } + public static String generateIdentifier(final String originalId, final String nsPrefix) { return String.format("%s::%s", nsPrefix, DHPUtils.md5(originalId)); } + public static String generateUnresolvedIdentifier(final String pid, final String pidType) { + + final String cleanedPid = CleaningFunctions.normalizePidValue(pidType, pid); + + return String.format("unresolved::%s::%s", cleanedPid, pidType.toLowerCase().trim()); + } + public static String getJPathString(final String jsonPath, final String json) { try { Object o = JsonPath.read(json, jsonPath); diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml index 2450bdad7..b1c8e7c85 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/publication/oozie_app/workflow.xml @@ -107,7 +107,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=2560 + --conf spark.sql.shuffle.partitions=5000 --inputGraphTablePath${inputGraphRootPath}/publication --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication @@ -159,7 +159,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=2560 + --conf spark.sql.shuffle.partitions=5000 --inputGraphTablePath${workingDir}/publication --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication diff --git a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml index a7dce8f2f..20ffe26d3 100644 --- a/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-actionmanager/src/main/resources/eu/dnetlib/dhp/actionmanager/wf/relation/oozie_app/workflow.xml @@ -99,7 +99,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=2560 + --conf spark.sql.shuffle.partitions=5000 --inputGraphTablePath${inputGraphRootPath}/relation --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Relation diff --git a/dhp-workflows/dhp-aggregation/pom.xml b/dhp-workflows/dhp-aggregation/pom.xml index 98e22d8a3..c89cc9d1d 100644 --- a/dhp-workflows/dhp-aggregation/pom.xml +++ b/dhp-workflows/dhp-aggregation/pom.xml @@ -29,6 +29,13 @@ testCompile + + scala-doc + process-resources + + doc + + ${scala.version} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/Constants.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/Constants.java new file mode 100644 index 000000000..c508d4dbc --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/Constants.java @@ -0,0 +1,49 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities; + +import java.util.Optional; + +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class Constants { + + public static final String DOI = "doi"; + + public static final String UPDATE_DATA_INFO_TYPE = "update"; + public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos"; + public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE"; + public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip"; + + public static final String FOS_CLASS_ID = "FOS"; + public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification"; + + public static final String NULL = "NULL"; + + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private Constants() { + } + + public static Boolean isSparkSessionManaged(ArgumentApplicationParser parser) { + return Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSData.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSData.java new file mode 100644 index 000000000..9dec3e862 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/GetFOSData.java @@ -0,0 +1,77 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities; + +import java.io.IOException; +import java.io.InputStreamReader; +import java.io.Serializable; +import java.util.Objects; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.collection.GetCSV; + +public class GetFOSData implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(GetFOSData.class); + + public static final char DEFAULT_DELIMITER = '\t'; + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + GetFOSData.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json")))); + + parser.parseArgument(args); + + // the path where the original fos csv file is stored + final String sourcePath = parser.get("sourcePath"); + log.info("sourcePath {}", sourcePath); + + // the path where to put the file as json + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}", outputPath); + + final String hdfsNameNode = parser.get("hdfsNameNode"); + log.info("hdfsNameNode {}", hdfsNameNode); + + final String classForName = parser.get("classForName"); + log.info("classForName {}", classForName); + + final char delimiter = Optional + .ofNullable(parser.get("delimiter")) + .map(s -> s.charAt(0)) + .orElse(DEFAULT_DELIMITER); + log.info("delimiter {}", delimiter); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + + new GetFOSData().doRewrite(sourcePath, outputPath, classForName, delimiter, fileSystem); + + } + + public void doRewrite(String inputPath, String outputFile, String classForName, char delimiter, FileSystem fs) + throws IOException, ClassNotFoundException { + + // reads the csv and writes it as its json equivalent + try (InputStreamReader reader = new InputStreamReader(fs.open(new Path(inputPath)))) { + GetCSV.getCsv(fs, reader, outputFile, classForName, delimiter); + } + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java new file mode 100644 index 000000000..3d68db27b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareBipFinder.java @@ -0,0 +1,145 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities; + +import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*; +import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.UPDATE_CLASS_NAME; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.hdfs.client.HdfsUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +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.actionmanager.createunresolvedentities.model.BipDeserialize; +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.BipScore; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.KeyValue; +import eu.dnetlib.dhp.schema.oaf.Measure; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.utils.DHPUtils; + +public class PrepareBipFinder implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(PrepareBipFinder.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + PrepareBipFinder.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_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 sourcePath = parser.get("sourcePath"); + log.info("sourcePath {}: ", sourcePath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + HdfsSupport.remove(outputPath, spark.sparkContext().hadoopConfiguration()); + prepareResults(spark, sourcePath, outputPath); + }); + } + + private static void prepareResults(SparkSession spark, String inputPath, String outputPath) { + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD bipDeserializeJavaRDD = sc + .textFile(inputPath) + .map(item -> OBJECT_MAPPER.readValue(item, BipDeserialize.class)); + + spark + .createDataset(bipDeserializeJavaRDD.flatMap(entry -> entry.keySet().stream().map(key -> { + BipScore bs = new BipScore(); + bs.setId(key); + bs.setScoreList(entry.get(key)); + return bs; + }).collect(Collectors.toList()).iterator()).rdd(), Encoders.bean(BipScore.class)) + .map((MapFunction) v -> { + Result r = new Result(); + + r.setId(DHPUtils.generateUnresolvedIdentifier(v.getId(), DOI)); + r.setMeasures(getMeasure(v)); + return r; + }, Encoders.bean(Result.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/bip"); + } + + private static List getMeasure(BipScore value) { + return value + .getScoreList() + .stream() + .map(score -> { + Measure m = new Measure(); + m.setId(score.getId()); + m + .setUnit( + score + .getUnit() + .stream() + .map(unit -> { + KeyValue kv = new KeyValue(); + kv.setValue(unit.getValue()); + kv.setKey(unit.getKey()); + kv + .setDataInfo( + OafMapperUtils + .dataInfo( + false, + UPDATE_DATA_INFO_TYPE, + true, + false, + OafMapperUtils + .qualifier( + UPDATE_MEASURE_BIP_CLASS_ID, + UPDATE_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS, + ModelConstants.DNET_PROVENANCE_ACTIONS), + "")); + return kv; + }) + .collect(Collectors.toList())); + return m; + }) + .collect(Collectors.toList()); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java new file mode 100644 index 000000000..5ae2f8c88 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareFOSSparkJob.java @@ -0,0 +1,133 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities; + +import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.*; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +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 eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import eu.dnetlib.dhp.utils.DHPUtils; + +public class PrepareFOSSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + PrepareFOSSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = isSparkSessionManaged(parser); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String sourcePath = parser.get("sourcePath"); + log.info("sourcePath: {}", sourcePath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + distributeFOSdois( + spark, + sourcePath, + + outputPath); + }); + } + + private static void distributeFOSdois(SparkSession spark, String sourcePath, String outputPath) { + Dataset fosDataset = readPath(spark, sourcePath, FOSDataModel.class); + + fosDataset.flatMap((FlatMapFunction) v -> { + List fosList = new ArrayList<>(); + final String level1 = v.getLevel1(); + final String level2 = v.getLevel2(); + final String level3 = v.getLevel3(); + Arrays + .stream(v.getDoi().split("\u0002")) + .forEach(d -> fosList.add(FOSDataModel.newInstance(d, level1, level2, level3))); + return fosList.iterator(); + }, Encoders.bean(FOSDataModel.class)) + .map((MapFunction) value -> { + Result r = new Result(); + r.setId(DHPUtils.generateUnresolvedIdentifier(value.getDoi(), DOI)); + r.setSubject(getSubjects(value)); + return r; + }, Encoders.bean(Result.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath + "/fos"); + } + + private static List getSubjects(FOSDataModel fos) { + return Arrays + .asList(getSubject(fos.getLevel1()), getSubject(fos.getLevel2()), getSubject(fos.getLevel3())) + .stream() + .filter(Objects::nonNull) + .collect(Collectors.toList()); + } + + private static StructuredProperty getSubject(String sbj) { + if (sbj.equals(NULL)) + return null; + StructuredProperty sp = new StructuredProperty(); + sp.setValue(sbj); + sp + .setQualifier( + OafMapperUtils + .qualifier( + FOS_CLASS_ID, + FOS_CLASS_NAME, + ModelConstants.DNET_SUBJECT_TYPOLOGIES, + ModelConstants.DNET_SUBJECT_TYPOLOGIES)); + sp + .setDataInfo( + OafMapperUtils + .dataInfo( + false, + UPDATE_DATA_INFO_TYPE, + true, + false, + OafMapperUtils + .qualifier( + UPDATE_SUBJECT_FOS_CLASS_ID, + UPDATE_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS, + ModelConstants.DNET_PROVENANCE_ACTIONS), + "")); + + return sp; + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java new file mode 100644 index 000000000..62b813602 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/SparkSaveUnresolved.java @@ -0,0 +1,79 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities; + +import static eu.dnetlib.dhp.actionmanager.createunresolvedentities.Constants.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +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 eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class SparkSaveUnresolved implements Serializable { + private static final Logger log = LoggerFactory.getLogger(PrepareFOSSparkJob.class); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + PrepareFOSSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/createunresolvedentities/produce_unresolved_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = isSparkSessionManaged(parser); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String sourcePath = parser.get("sourcePath"); + log.info("sourcePath: {}", sourcePath); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + saveUnresolved( + spark, + sourcePath, + + outputPath); + }); + } + + private static void saveUnresolved(SparkSession spark, String sourcePath, String outputPath) { + + spark + .read() + .textFile(sourcePath + "/*") + .map( + (MapFunction) l -> OBJECT_MAPPER.readValue(l, Result.class), + Encoders.bean(Result.class)) + .groupByKey((MapFunction) r -> r.getId(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> { + Result ret = it.next(); + it.forEachRemaining(r -> ret.mergeFrom(r)); + return ret; + }, Encoders.bean(Result.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(outputPath); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipDeserialize.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipDeserialize.java new file mode 100644 index 000000000..f950d9260 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipDeserialize.java @@ -0,0 +1,28 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.HashMap; +import java.util.List; + +/** + * Class that maps the model of the bipFinder! input data. + * Only needed for deserialization purposes + */ + +public class BipDeserialize extends HashMap> implements Serializable { + + public BipDeserialize() { + super(); + } + + public List get(String key) { + + if (super.get(key) == null) { + return new ArrayList<>(); + } + return super.get(key); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipScore.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipScore.java new file mode 100644 index 000000000..c36856a5b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/BipScore.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model; + +import java.io.Serializable; +import java.util.List; + +/** + * Rewriting of the bipFinder input data by extracting the identifier of the result (doi) + */ + +public class BipScore implements Serializable { + private String id; // doi + private List scoreList; // unit as given in the inputfile + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getScoreList() { + return scoreList; + } + + public void setScoreList(List scoreList) { + this.scoreList = scoreList; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java new file mode 100644 index 000000000..befb230cb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/FOSDataModel.java @@ -0,0 +1,71 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model; + +import java.io.Serializable; + +import com.opencsv.bean.CsvBindByPosition; + +public class FOSDataModel implements Serializable { + @CsvBindByPosition(position = 1) +// @CsvBindByName(column = "doi") + private String doi; + + @CsvBindByPosition(position = 2) +// @CsvBindByName(column = "level1") + private String level1; + + @CsvBindByPosition(position = 3) +// @CsvBindByName(column = "level2") + private String level2; + + @CsvBindByPosition(position = 4) +// @CsvBindByName(column = "level3") + private String level3; + + public FOSDataModel() { + + } + + public FOSDataModel(String doi, String level1, String level2, String level3) { + this.doi = doi; + this.level1 = level1; + this.level2 = level2; + this.level3 = level3; + } + + public static FOSDataModel newInstance(String d, String level1, String level2, String level3) { + return new FOSDataModel(d, level1, level2, level3); + } + + public String getDoi() { + return doi; + } + + public void setDoi(String doi) { + this.doi = doi; + } + + public String getLevel1() { + return level1; + } + + public void setLevel1(String level1) { + this.level1 = level1; + } + + public String getLevel2() { + return level2; + } + + public void setLevel2(String level2) { + this.level2 = level2; + } + + public String getLevel3() { + return level3; + } + + public void setLevel3(String level3) { + this.level3 = level3; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/KeyValue.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/KeyValue.java new file mode 100644 index 000000000..4384e4ba1 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/KeyValue.java @@ -0,0 +1,26 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model; + +import java.io.Serializable; + +public class KeyValue implements Serializable { + + private String key; + private String value; + + public String getKey() { + return key; + } + + public void setKey(String key) { + this.key = key; + } + + public String getValue() { + return value; + } + + public void setValue(String value) { + this.value = value; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/Score.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/Score.java new file mode 100644 index 000000000..3d1cca9a0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/model/Score.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities.model; + +import java.io.Serializable; +import java.util.List; + +/** + * represents the score in the input file + */ +public class Score implements Serializable { + + private String id; + private List unit; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public List getUnit() { + return unit; + } + + public void setUnit(List unit) { + this.unit = unit; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala deleted file mode 100644 index 9f0d25735..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ExportActionSetJobNode.scala +++ /dev/null @@ -1,41 +0,0 @@ -package eu.dnetlib.dhp.actionmanager.datacite - -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.Oaf -import org.apache.hadoop.io.Text -import org.apache.hadoop.io.compress.GzipCodec -import org.apache.hadoop.mapred.SequenceFileOutputFormat -import org.apache.spark.SparkConf -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} -import org.slf4j.{Logger, LoggerFactory} - -import scala.io.Source - -object ExportActionSetJobNode { - - val log: Logger = LoggerFactory.getLogger(ExportActionSetJobNode.getClass) - - def main(args: Array[String]): Unit = { - val conf = new SparkConf - val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json")).mkString) - parser.parseArgument(args) - val master = parser.get("master") - val sourcePath = parser.get("sourcePath") - val targetPath = parser.get("targetPath") - - val spark: SparkSession = SparkSession.builder().config(conf) - .appName(ExportActionSetJobNode.getClass.getSimpleName) - .master(master) - .getOrCreate() - implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] - implicit val tEncoder:Encoder[(String,String)] = Encoders.tuple(Encoders.STRING,Encoders.STRING) - - spark.read.load(sourcePath).as[Oaf] - .map(o =>DataciteToOAFTransformation.toActionSet(o)) - .filter(o => o!= null) - .rdd.map(s => (new Text(s._1), new Text(s._2))).saveAsHadoopFile(s"$targetPath", classOf[Text], classOf[Text], classOf[SequenceFileOutputFormat[Text,Text]], classOf[GzipCodec]) - - - } - -} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/FilterCrossrefEntitiesSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/FilterCrossrefEntitiesSpark.scala deleted file mode 100644 index 5860c50ac..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/FilterCrossrefEntitiesSpark.scala +++ /dev/null @@ -1,46 +0,0 @@ -package eu.dnetlib.dhp.actionmanager.datacite - -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup -import eu.dnetlib.dhp.schema.mdstore.MetadataRecord -import eu.dnetlib.dhp.schema.oaf.{Oaf, Result} -import eu.dnetlib.dhp.utils.ISLookupClientFactory -import org.apache.spark.SparkConf -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} -import org.slf4j.{Logger, LoggerFactory} - -import scala.io.Source - -object FilterCrossrefEntitiesSpark { - - val log: Logger = LoggerFactory.getLogger(getClass.getClass) - - def main(args: Array[String]): Unit = { - val conf = new SparkConf - val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/filter_crossref_param.json")).mkString) - parser.parseArgument(args) - val master = parser.get("master") - val sourcePath = parser.get("sourcePath") - log.info("sourcePath: {}", sourcePath) - val targetPath = parser.get("targetPath") - log.info("targetPath: {}", targetPath) - - - - val spark: SparkSession = SparkSession.builder().config(conf) - .appName(getClass.getSimpleName) - .master(master) - .getOrCreate() - - - - implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] - implicit val resEncoder: Encoder[Result] = Encoders.kryo[Result] - - val d:Dataset[Oaf]= spark.read.load(sourcePath).as[Oaf] - - d.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result]).write.mode(SaveMode.Overwrite).save(targetPath) - - } - -} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala deleted file mode 100644 index 2cabc7879..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/GenerateDataciteDatasetSpark.scala +++ /dev/null @@ -1,48 +0,0 @@ -package eu.dnetlib.dhp.actionmanager.datacite - -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup -import eu.dnetlib.dhp.schema.mdstore.MetadataRecord -import eu.dnetlib.dhp.schema.oaf.Oaf -import eu.dnetlib.dhp.utils.ISLookupClientFactory -import org.apache.spark.SparkConf -import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} -import org.slf4j.{Logger, LoggerFactory} - -import scala.io.Source - -object GenerateDataciteDatasetSpark { - - val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass) - - def main(args: Array[String]): Unit = { - val conf = new SparkConf - val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString) - parser.parseArgument(args) - val master = parser.get("master") - val sourcePath = parser.get("sourcePath") - val targetPath = parser.get("targetPath") - val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks")) - val isLookupUrl: String = parser.get("isLookupUrl") - log.info("isLookupUrl: {}", isLookupUrl) - - val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl) - val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService) - val spark: SparkSession = SparkSession.builder().config(conf) - .appName(GenerateDataciteDatasetSpark.getClass.getSimpleName) - .master(master) - .getOrCreate() - - implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord] - - implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] - - import spark.implicits._ - - spark.read.load(sourcePath).as[DataciteType] - .filter(d => d.isActive) - .flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks)) - .filter(d => d != null) - .write.mode(SaveMode.Overwrite).save(targetPath) - } -} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java new file mode 100644 index 000000000..ea5fea96f --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateActionSetSparkJob.java @@ -0,0 +1,181 @@ + +package eu.dnetlib.dhp.actionmanager.opencitations; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.IOException; +import java.io.Serializable; +import java.util.*; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.FlatMapFunction; +import org.apache.spark.sql.Encoders; +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.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; +import scala.Tuple2; + +public class CreateActionSetSparkJob implements Serializable { + public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations"; + public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations"; + private static final String ID_PREFIX = "50|doi_________::"; + private static final String TRUST = "0.91"; + + private static final Logger log = LoggerFactory.getLogger(CreateActionSetSparkJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(final String[] args) throws IOException, ParseException { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + CreateActionSetSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json")))); + + 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("inputPath"); + log.info("inputPath {}", inputPath.toString()); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}", outputPath); + + final boolean shouldDuplicateRels = Optional + .ofNullable(parser.get("shouldDuplicateRels")) + .map(Boolean::valueOf) + .orElse(Boolean.FALSE); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + extractContent(spark, inputPath, outputPath, shouldDuplicateRels); + }); + + } + + private static void extractContent(SparkSession spark, String inputPath, String outputPath, + boolean shouldDuplicateRels) { + spark + .sqlContext() + .createDataset(spark.sparkContext().textFile(inputPath + "/*", 6000), Encoders.STRING()) + .flatMap( + (FlatMapFunction) value -> createRelation(value, shouldDuplicateRels).iterator(), + Encoders.bean(Relation.class)) + .filter((FilterFunction) value -> value != null) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + + } + + private static List createRelation(String value, boolean duplicate) { + String[] line = value.split(","); + if (!line[1].startsWith("10.")) { + return new ArrayList<>(); + } + List relationList = new ArrayList<>(); + + String citing = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[1])); + final String cited = ID_PREFIX + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", line[2])); + + relationList + .addAll( + getRelations( + citing, + cited)); + + if (duplicate && line[1].endsWith(".refs")) { + citing = ID_PREFIX + IdentifierFactory + .md5(CleaningFunctions.normalizePidValue("doi", line[1].substring(0, line[1].indexOf(".refs")))); + relationList.addAll(getRelations(citing, cited)); + } + + return relationList; + } + + private static Collection getRelations(String citing, String cited) { + + return Arrays + .asList( + getRelation(citing, cited, ModelConstants.CITES), + getRelation(cited, citing, ModelConstants.IS_CITED_BY)); + } + + public static Relation getRelation( + String source, + String target, + String relclass) { + Relation r = new Relation(); + r.setCollectedfrom(getCollectedFrom()); + r.setSource(source); + r.setTarget(target); + r.setRelClass(relclass); + r.setRelType(ModelConstants.RESULT_RESULT); + r.setSubRelType(ModelConstants.CITATION); + r + .setDataInfo( + getDataInfo()); + return r; + } + + public static List getCollectedFrom() { + KeyValue kv = new KeyValue(); + kv.setKey(ModelConstants.OPENOCITATIONS_ID); + kv.setValue(ModelConstants.OPENOCITATIONS_NAME); + + return Arrays.asList(kv); + } + + public static DataInfo getDataInfo() { + DataInfo di = new DataInfo(); + di.setInferred(false); + di.setDeletedbyinference(false); + di.setTrust(TRUST); + + di + .setProvenanceaction( + getQualifier(OPENCITATIONS_CLASSID, OPENCITATIONS_CLASSNAME, ModelConstants.DNET_PROVENANCE_ACTIONS)); + return di; + } + + public static Qualifier getQualifier(String class_id, String class_name, + String qualifierSchema) { + Qualifier pa = new Qualifier(); + pa.setClassid(class_id); + pa.setClassname(class_name); + pa.setSchemeid(qualifierSchema); + pa.setSchemename(qualifierSchema); + return pa; + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java new file mode 100644 index 000000000..3530c9980 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/opencitations/GetOpenCitationsRefs.java @@ -0,0 +1,93 @@ + +package eu.dnetlib.dhp.actionmanager.opencitations; + +import java.io.*; +import java.io.Serializable; +import java.util.Objects; +import java.util.zip.GZIPOutputStream; +import java.util.zip.ZipEntry; +import java.util.zip.ZipInputStream; + +import org.apache.commons.cli.ParseException; +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FSDataInputStream; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class GetOpenCitationsRefs implements Serializable { + private static final Logger log = LoggerFactory.getLogger(GetOpenCitationsRefs.class); + + public static void main(final String[] args) throws IOException, ParseException { + + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + Objects + .requireNonNull( + GetOpenCitationsRefs.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json")))); + + parser.parseArgument(args); + + final String[] inputFile = parser.get("inputFile").split(";"); + log.info("inputFile {}", inputFile.toString()); + + final String workingPath = parser.get("workingPath"); + log.info("workingPath {}", workingPath); + + final String hdfsNameNode = parser.get("hdfsNameNode"); + log.info("hdfsNameNode {}", hdfsNameNode); + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + + GetOpenCitationsRefs ocr = new GetOpenCitationsRefs(); + + for (String file : inputFile) { + ocr.doExtract(workingPath + "/Original/" + file, workingPath, fileSystem); + } + + } + + private void doExtract(String inputFile, String workingPath, FileSystem fileSystem) + throws IOException { + + final Path path = new Path(inputFile); + + FSDataInputStream oc_zip = fileSystem.open(path); + + int count = 1; + try (ZipInputStream zis = new ZipInputStream(oc_zip)) { + ZipEntry entry = null; + while ((entry = zis.getNextEntry()) != null) { + + if (!entry.isDirectory()) { + String fileName = entry.getName(); + fileName = fileName.substring(0, fileName.indexOf("T")) + "_" + count; + count++; + try ( + FSDataOutputStream out = fileSystem + .create(new Path(workingPath + "/COCI/" + fileName + ".gz")); + GZIPOutputStream gzipOs = new GZIPOutputStream(new BufferedOutputStream(out))) { + + IOUtils.copy(zis, gzipOs); + + } + } + + } + + } + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala index b78f411ee..7a87861db 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/scholix/SparkCreateActionset.scala @@ -60,14 +60,10 @@ object SparkCreateActionset { val entities: Dataset[(String, Result)] = spark.read.load(s"$sourcePath/entities/*").as[Result].map(p => (p.getId, p))(Encoders.tuple(Encoders.STRING, resultEncoders)) - - entities.filter(r => r.isInstanceOf[Result]).map(r => r.asInstanceOf[Result]) entities .joinWith(idRelation, entities("_1").equalTo(idRelation("value"))) .map(p => p._1._2) .write.mode(SaveMode.Append).save(s"$workingDirFolder/actionSetOaf") - - } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala new file mode 100644 index 000000000..11ecfd6cb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectionUtils.scala @@ -0,0 +1,49 @@ +package eu.dnetlib.dhp.collection + +import eu.dnetlib.dhp.schema.common.ModelSupport +import eu.dnetlib.dhp.schema.oaf.{Oaf, OafEntity, Relation} + +object CollectionUtils { + + /** + * This method in pipeline to the transformation phase, + * generates relations in both verse, typically it should be a phase of flatMap + * + * @param i input OAF + * @return + * If the input OAF is an entity -> List(i) + * If the input OAF is a relation -> List(relation, inverseRelation) + * + */ + + def fixRelations(i: Oaf): List[Oaf] = { + if (i.isInstanceOf[OafEntity]) + return List(i) + else { + val r: Relation = i.asInstanceOf[Relation] + val currentRel = ModelSupport.findRelation(r.getRelClass) + if (currentRel != null) { + + // Cleaning relation + r.setRelType(currentRel.getRelType) + r.setSubRelType(currentRel.getSubReltype) + r.setRelClass(currentRel.getRelClass) + val inverse = new Relation + inverse.setSource(r.getTarget) + inverse.setTarget(r.getSource) + inverse.setRelType(currentRel.getRelType) + inverse.setSubRelType(currentRel.getSubReltype) + inverse.setRelClass(currentRel.getInverseRelClass) + inverse.setCollectedfrom(r.getCollectedfrom) + inverse.setDataInfo(r.getDataInfo) + inverse.setProperties(r.getProperties) + inverse.setLastupdatetimestamp(r.getLastupdatetimestamp) + inverse.setValidated(r.getValidated) + inverse.setValidationDate(r.getValidationDate) + return List(r, inverse) + } + } + List() + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/AbstractRestClient.scala similarity index 90% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/AbstractRestClient.scala index bae41b218..6a9b8e3e5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/AbstractRestClient.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/AbstractRestClient.scala @@ -1,12 +1,10 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite import org.apache.commons.io.IOUtils import org.apache.http.client.config.RequestConfig -import org.apache.http.client.methods.{HttpGet, HttpPost, HttpRequestBase, HttpUriRequest} +import org.apache.http.client.methods.{HttpGet, HttpPost, HttpUriRequest} import org.apache.http.entity.StringEntity -import org.apache.http.impl.client.{HttpClientBuilder, HttpClients} - -import java.io.IOException +import org.apache.http.impl.client.HttpClientBuilder abstract class AbstractRestClient extends Iterator[String] { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteAPIImporter.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala similarity index 95% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteAPIImporter.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala index 36ec9e8c3..7ec44a6ff 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteAPIImporter.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteAPIImporter.scala @@ -1,7 +1,7 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite -import org.json4s.{DefaultFormats, JValue} import org.json4s.jackson.JsonMethods.{compact, parse, render} +import org.json4s.{DefaultFormats, JValue} class DataciteAPIImporter(timestamp: Long = 0, blocks: Long = 10, until:Long = -1) extends AbstractRestClient { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala new file mode 100644 index 000000000..0685a04a3 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteModelConstants.scala @@ -0,0 +1,134 @@ +package eu.dnetlib.dhp.datacite + +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{DataInfo, KeyValue} +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils + +import java.io.InputStream +import java.time.format.DateTimeFormatter +import java.util.Locale +import java.util.regex.Pattern +import scala.io.Source + +/** + * This class represent the dataModel of the input Dataset of Datacite + * @param doi THE DOI + * @param timestamp timestamp of last update date + * @param isActive the record is active or deleted + * @param json the json native records + */ +case class DataciteType(doi: String, timestamp: Long, isActive: Boolean, json: String) {} + +/* + The following class are utility class used for the mapping from + json datacite to OAF Shema + */ +case class RelatedIdentifierType(relationType: String, relatedIdentifier: String, relatedIdentifierType: String) {} + +case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {} + +case class CreatorType(nameType: Option[String], nameIdentifiers: Option[List[NameIdentifiersType]], name: Option[String], familyName: Option[String], givenName: Option[String], affiliation: Option[List[String]]) {} + +case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {} + +case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {} + +case class DescriptionType(descriptionType: Option[String], description: Option[String]) {} + +case class FundingReferenceType(funderIdentifierType: Option[String], awardTitle: Option[String], awardUri: Option[String], funderName: Option[String], funderIdentifier: Option[String], awardNumber: Option[String]) {} + +case class DateType(date: Option[String], dateType: Option[String]) {} + +case class OAFRelations(relation:String, inverse:String, relType:String) + + +class DataciteModelConstants extends Serializable { + +} + +object DataciteModelConstants { + + val REL_TYPE_VALUE:String = "resultResult" + val DATE_RELATION_KEY = "RelationDate" + val DATACITE_FILTER_PATH = "/eu/dnetlib/dhp/datacite/datacite_filter" + val DOI_CLASS = "doi" + val SUBJ_CLASS = "keywords" + val DATACITE_NAME = "Datacite" + val dataInfo: DataInfo = dataciteDataInfo("0.9") + val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, DATACITE_NAME) + + val subRelTypeMapping: Map[String,OAFRelations] = Map( + ModelConstants.REFERENCES -> OAFRelations(ModelConstants.REFERENCES, ModelConstants.IS_REFERENCED_BY, ModelConstants.RELATIONSHIP), + ModelConstants.IS_REFERENCED_BY -> OAFRelations(ModelConstants.IS_REFERENCED_BY,ModelConstants.REFERENCES, ModelConstants.RELATIONSHIP), + + ModelConstants.IS_SUPPLEMENTED_BY -> OAFRelations(ModelConstants.IS_SUPPLEMENTED_BY,ModelConstants.IS_SUPPLEMENT_TO,ModelConstants.SUPPLEMENT), + ModelConstants.IS_SUPPLEMENT_TO -> OAFRelations(ModelConstants.IS_SUPPLEMENT_TO,ModelConstants.IS_SUPPLEMENTED_BY,ModelConstants.SUPPLEMENT), + + ModelConstants.HAS_PART -> OAFRelations(ModelConstants.HAS_PART,ModelConstants.IS_PART_OF, ModelConstants.PART), + ModelConstants.IS_PART_OF -> OAFRelations(ModelConstants.IS_PART_OF,ModelConstants.HAS_PART, ModelConstants.PART), + + ModelConstants.IS_VERSION_OF-> OAFRelations(ModelConstants.IS_VERSION_OF,ModelConstants.HAS_VERSION,ModelConstants.VERSION), + ModelConstants.HAS_VERSION-> OAFRelations(ModelConstants.HAS_VERSION,ModelConstants.IS_VERSION_OF,ModelConstants.VERSION), + + ModelConstants.IS_IDENTICAL_TO -> OAFRelations(ModelConstants.IS_IDENTICAL_TO,ModelConstants.IS_IDENTICAL_TO, ModelConstants.RELATIONSHIP), + + ModelConstants.IS_CONTINUED_BY -> OAFRelations(ModelConstants.IS_CONTINUED_BY,ModelConstants.CONTINUES, ModelConstants.RELATIONSHIP), + ModelConstants.CONTINUES -> OAFRelations(ModelConstants.CONTINUES,ModelConstants.IS_CONTINUED_BY, ModelConstants.RELATIONSHIP), + + ModelConstants.IS_NEW_VERSION_OF-> OAFRelations(ModelConstants.IS_NEW_VERSION_OF,ModelConstants.IS_PREVIOUS_VERSION_OF, ModelConstants.VERSION), + ModelConstants.IS_PREVIOUS_VERSION_OF ->OAFRelations(ModelConstants.IS_PREVIOUS_VERSION_OF,ModelConstants.IS_NEW_VERSION_OF, ModelConstants.VERSION), + + ModelConstants.IS_DOCUMENTED_BY -> OAFRelations(ModelConstants.IS_DOCUMENTED_BY,ModelConstants.DOCUMENTS, ModelConstants.RELATIONSHIP), + ModelConstants.DOCUMENTS -> OAFRelations(ModelConstants.DOCUMENTS,ModelConstants.IS_DOCUMENTED_BY, ModelConstants.RELATIONSHIP), + + ModelConstants.IS_SOURCE_OF -> OAFRelations(ModelConstants.IS_SOURCE_OF,ModelConstants.IS_DERIVED_FROM, ModelConstants.VERSION), + ModelConstants.IS_DERIVED_FROM -> OAFRelations(ModelConstants.IS_DERIVED_FROM,ModelConstants.IS_SOURCE_OF, ModelConstants.VERSION), + + ModelConstants.CITES -> OAFRelations(ModelConstants.CITES,ModelConstants.IS_CITED_BY, ModelConstants.CITATION), + ModelConstants.IS_CITED_BY -> OAFRelations(ModelConstants.IS_CITED_BY,ModelConstants.CITES, ModelConstants.CITATION), + + ModelConstants.IS_VARIANT_FORM_OF -> OAFRelations(ModelConstants.IS_VARIANT_FORM_OF,ModelConstants.IS_DERIVED_FROM, ModelConstants.VERSION), + ModelConstants.IS_OBSOLETED_BY -> OAFRelations(ModelConstants.IS_OBSOLETED_BY,ModelConstants.IS_NEW_VERSION_OF, ModelConstants.VERSION), + + ModelConstants.REVIEWS -> OAFRelations(ModelConstants.REVIEWS,ModelConstants.IS_REVIEWED_BY, ModelConstants.REVIEW), + ModelConstants.IS_REVIEWED_BY -> OAFRelations(ModelConstants.IS_REVIEWED_BY,ModelConstants.REVIEWS, ModelConstants.REVIEW), + + ModelConstants.DOCUMENTS -> OAFRelations(ModelConstants.DOCUMENTS,ModelConstants.IS_DOCUMENTED_BY, ModelConstants.RELATIONSHIP), + ModelConstants.IS_DOCUMENTED_BY -> OAFRelations(ModelConstants.IS_DOCUMENTED_BY,ModelConstants.DOCUMENTS, ModelConstants.RELATIONSHIP), + + ModelConstants.COMPILES -> OAFRelations(ModelConstants.COMPILES,ModelConstants.IS_COMPILED_BY, ModelConstants.RELATIONSHIP), + ModelConstants.IS_COMPILED_BY -> OAFRelations(ModelConstants.IS_COMPILED_BY,ModelConstants.COMPILES, ModelConstants.RELATIONSHIP) + ) + + + val datacite_filter: List[String] = { + val stream: InputStream = getClass.getResourceAsStream(DATACITE_FILTER_PATH) + require(stream!= null) + Source.fromInputStream(stream).getLines().toList + } + + + def dataciteDataInfo(trust: String): DataInfo = OafMapperUtils.dataInfo(false,null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, trust) + + val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern("[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]", Locale.ENGLISH) + val df_it: DateTimeFormatter = DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN) + + val funder_regex: List[(Pattern, String)] = List( + (Pattern.compile("(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda__h2020::"), + (Pattern.compile("(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda_______::") + + ) + + val Date_regex: List[Pattern] = List( + //Y-M-D + Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE), + //M-D-Y + Pattern.compile("((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d", Pattern.MULTILINE), + //D-M-Y + Pattern.compile("(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})", Pattern.MULTILINE), + //Y + Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE) + ) + + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala similarity index 74% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index cfdd98d30..6b4deef0a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -1,7 +1,8 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup +import eu.dnetlib.dhp.datacite.DataciteModelConstants._ import eu.dnetlib.dhp.schema.action.AtomicAction import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils} @@ -12,121 +13,30 @@ import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse -import java.nio.charset.CodingErrorAction import java.text.SimpleDateFormat import java.time.LocalDate import java.time.chrono.ThaiBuddhistDate import java.time.format.DateTimeFormatter -import java.util.regex.Pattern import java.util.{Date, Locale} import scala.collection.JavaConverters._ -import scala.io.{Codec, Source} -import scala.language.postfixOps -case class DataciteType(doi: String, timestamp: Long, isActive: Boolean, json: String) {} - -case class RelatedIdentifierType(relationType: String, relatedIdentifier: String, relatedIdentifierType: String) {} - -case class NameIdentifiersType(nameIdentifierScheme: Option[String], schemeUri: Option[String], nameIdentifier: Option[String]) {} - -case class CreatorType(nameType: Option[String], nameIdentifiers: Option[List[NameIdentifiersType]], name: Option[String], familyName: Option[String], givenName: Option[String], affiliation: Option[List[String]]) {} - -case class TitleType(title: Option[String], titleType: Option[String], lang: Option[String]) {} - -case class SubjectType(subject: Option[String], subjectScheme: Option[String]) {} - -case class DescriptionType(descriptionType: Option[String], description: Option[String]) {} - -case class FundingReferenceType(funderIdentifierType: Option[String], awardTitle: Option[String], awardUri: Option[String], funderName: Option[String], funderIdentifier: Option[String], awardNumber: Option[String]) {} - -case class DateType(date: Option[String], dateType: Option[String]) {} - -case class HostedByMapType(openaire_id: String, datacite_name: String, official_name: String, similarity: Option[Float]) {} object DataciteToOAFTransformation { - val REL_TYPE_VALUE:String = "resultResult" - val DATE_RELATION_KEY = "RelationDate" - - val subRelTypeMapping: Map[String,(String,String)] = Map( - "References" ->("IsReferencedBy","relationship"), - "IsSupplementTo" ->("IsSupplementedBy","supplement"), - "IsPartOf" ->("HasPart","part"), - "HasPart" ->("IsPartOf","part"), - "IsVersionOf" ->("HasVersion","version"), - "HasVersion" ->("IsVersionOf","version"), - "IsIdenticalTo" ->("IsIdenticalTo","relationship"), - "IsPreviousVersionOf" ->("IsNewVersionOf","version"), - "IsContinuedBy" ->("Continues","relationship"), - "Continues" ->("IsContinuedBy","relationship"), - "IsNewVersionOf" ->("IsPreviousVersionOf","version"), - "IsSupplementedBy" ->("IsSupplementTo","supplement"), - "IsDocumentedBy" ->("Documents","relationship"), - "IsSourceOf" ->("IsDerivedFrom","relationship"), - "Cites" ->("IsCitedBy","citation"), - "IsCitedBy" ->("Cites","citation"), - "IsDerivedFrom" ->("IsSourceOf","relationship"), - "IsVariantFormOf" ->("IsDerivedFrom","version"), - "IsReferencedBy" ->("References","relationship"), - "IsObsoletedBy" ->("IsNewVersionOf","version"), - "Reviews" ->("IsReviewedBy","review"), - "Documents" ->("IsDocumentedBy","relationship"), - "IsCompiledBy" ->("Compiles","relationship"), - "Compiles" ->("IsCompiledBy","relationship"), - "IsReviewedBy" ->("Reviews","review") - ) - - implicit val codec: Codec = Codec("UTF-8") - codec.onMalformedInput(CodingErrorAction.REPLACE) - codec.onUnmappableCharacter(CodingErrorAction.REPLACE) - - val DOI_CLASS = "doi" - val SUBJ_CLASS = "keywords" - - - val j_filter: List[String] = { - val s = Source.fromInputStream(getClass.getResourceAsStream("datacite_filter")).mkString - s.lines.toList - } - val mapper = new ObjectMapper() - val unknown_repository: HostedByMapType = HostedByMapType(ModelConstants.UNKNOWN_REPOSITORY_ORIGINALID, ModelConstants.UNKNOWN_REPOSITORY.getValue, ModelConstants.UNKNOWN_REPOSITORY.getValue, Some(1.0F)) - val dataInfo: DataInfo = generateDataInfo("0.9") - val DATACITE_COLLECTED_FROM: KeyValue = OafMapperUtils.keyValue(ModelConstants.DATACITE_ID, "Datacite") - val hostedByMap: Map[String, HostedByMapType] = { - val s = Source.fromInputStream(getClass.getResourceAsStream("hostedBy_map.json")).mkString - implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - lazy val json: org.json4s.JValue = parse(s) - json.extract[Map[String, HostedByMapType]] - } - - val df_en: DateTimeFormatter = DateTimeFormatter.ofPattern("[MM-dd-yyyy][MM/dd/yyyy][dd-MM-yy][dd-MMM-yyyy][dd/MMM/yyyy][dd-MMM-yy][dd/MMM/yy][dd-MM-yy][dd/MM/yy][dd-MM-yyyy][dd/MM/yyyy][yyyy-MM-dd][yyyy/MM/dd]", Locale.ENGLISH) - val df_it: DateTimeFormatter = DateTimeFormatter.ofPattern("[dd-MM-yyyy][dd/MM/yyyy]", Locale.ITALIAN) - - val funder_regex: List[(Pattern, String)] = List( - (Pattern.compile("(info:eu-repo/grantagreement/ec/h2020/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda__h2020::"), - (Pattern.compile("(info:eu-repo/grantagreement/ec/fp7/)(\\d\\d\\d\\d\\d\\d)(.*)", Pattern.MULTILINE | Pattern.CASE_INSENSITIVE), "40|corda_______::") - - ) - - val Date_regex: List[Pattern] = List( - //Y-M-D - Pattern.compile("(18|19|20)\\d\\d([- /.])(0[1-9]|1[012])\\2(0[1-9]|[12][0-9]|3[01])", Pattern.MULTILINE), - //M-D-Y - Pattern.compile("((0[1-9]|1[012])|([1-9]))([- /.])(0[1-9]|[12][0-9]|3[01])([- /.])(18|19|20)?\\d\\d", Pattern.MULTILINE), - //D-M-Y - Pattern.compile("(?:(?:31(/|-|\\.)(?:0?[13578]|1[02]|(?:Jan|Mar|May|Jul|Aug|Oct|Dec)))\\1|(?:(?:29|30)(/|-|\\.)(?:0?[1,3-9]|1[0-2]|(?:Jan|Mar|Apr|May|Jun|Jul|Aug|Sep|Oct|Nov|Dec))\\2))(?:(?:1[6-9]|[2-9]\\d)?\\d{2})|(?:29(/|-|\\.)(?:0?2|(?:Feb))\\3(?:(?:(?:1[6-9]|[2-9]\\d)?(?:0[48]|[2468][048]|[13579][26])|(?:(?:16|[2468][048]|[3579][26])00))))|(?:0?[1-9]|1\\d|2[0-8])(/|-|\\.)(?:(?:0?[1-9]|(?:Jan|Feb|Mar|Apr|May|Jun|Jul|Aug|Sep))|(?:1[0-2]|(?:Oct|Nov|Dec)))\\4(?:(?:1[6-9]|[2-9]\\d)?\\d{2})", Pattern.MULTILINE), - //Y - Pattern.compile("(19|20)\\d\\d", Pattern.MULTILINE) - ) - - - def filter_json(json: String): Boolean = { - j_filter.exists(f => json.contains(f)) + /** + * This method should skip record if json contains invalid text + * defined in gile datacite_filter + * @param json + * @return True if the record should be skipped + */ + def skip_record(json: String): Boolean = { + datacite_filter.exists(f => json.contains(f)) } + @deprecated("this method will be removed", "dhp") def toActionSet(item: Oaf): (String, String) = { val mapper = new ObjectMapper() @@ -206,6 +116,8 @@ object DataciteToOAFTransformation { case _: Throwable => "" } } + + def getTypeQualifier(resourceType: String, resourceTypeGeneral: String, schemaOrg: String, vocabularies: VocabularyGroup): (Qualifier, Qualifier) = { if (resourceType != null && resourceType.nonEmpty) { val typeQualifier = vocabularies.getSynonymAsQualifier(ModelConstants.DNET_PUBLICATION_RESOURCE, resourceType) @@ -324,10 +236,7 @@ object DataciteToOAFTransformation { val p = match_pattern.get._2 val grantId = m.matcher(awardUri).replaceAll("$2") val targetId = s"$p${DHPUtils.md5(grantId)}" - List( - generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo), - generateRelation(targetId, sourceId, "produces", DATACITE_COLLECTED_FROM, dataInfo) - ) + List( generateRelation(sourceId, targetId, "isProducedBy", DATACITE_COLLECTED_FROM, dataInfo) ) } else List() @@ -336,7 +245,7 @@ object DataciteToOAFTransformation { def generateOAF(input: String, ts: Long, dateOfCollection: Long, vocabularies: VocabularyGroup, exportLinks: Boolean): List[Oaf] = { - if (filter_json(input)) + if (skip_record(input)) return List() implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats @@ -515,8 +424,8 @@ object DataciteToOAFTransformation { val access_rights_qualifier = if (aRights.isDefined) aRights.get else OafMapperUtils.accessRight(ModelConstants.UNKNOWN, ModelConstants.NOT_AVAILABLE, ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES) if (client.isDefined) { - val hb = hostedByMap.getOrElse(client.get.toUpperCase(), unknown_repository) - instance.setHostedby(OafMapperUtils.keyValue(generateDSId(hb.openaire_id), hb.official_name)) + + instance.setHostedby(OafMapperUtils.keyValue(generateDSId(ModelConstants.UNKNOWN_REPOSITORY_ORIGINALID), ModelConstants.UNKNOWN_REPOSITORY.getValue)) instance.setCollectedfrom(DATACITE_COLLECTED_FROM) instance.setUrl(List(s"https://dx.doi.org/$doi").asJava) instance.setAccessright(access_rights_qualifier) @@ -570,7 +479,7 @@ object DataciteToOAFTransformation { rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava) rel.setDataInfo(dataInfo) - val subRelType = subRelTypeMapping(r.relationType)._2 + val subRelType = subRelTypeMapping(r.relationType).relType rel.setRelType(REL_TYPE_VALUE) rel.setSubRelType(subRelType) rel.setRelClass(r.relationType) @@ -580,22 +489,13 @@ object DataciteToOAFTransformation { rel.setProperties(List(dateProps).asJava) rel.setSource(id) - rel.setTarget(s"unresolved::${r.relatedIdentifier}::${r.relatedIdentifierType}") + rel.setTarget(DHPUtils.generateUnresolvedIdentifier(r.relatedIdentifier,r.relatedIdentifierType)) rel.setCollectedfrom(List(DATACITE_COLLECTED_FROM).asJava) - rel.getCollectedfrom.asScala.map(c => c.getValue)(collection.breakOut) + rel.getCollectedfrom.asScala.map(c => c.getValue).toList rel - })(collection breakOut) + }) } - def generateDataInfo(trust: String): DataInfo = { - val di = new DataInfo - di.setDeletedbyinference(false) - di.setInferred(false) - di.setInvisible(false) - di.setTrust(trust) - di.setProvenanceaction(ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER) - di - } def generateDSId(input: String): String = { val b = StringUtils.substringBefore(input, "::") diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala new file mode 100644 index 000000000..e1607ee9c --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/GenerateDataciteDatasetSpark.scala @@ -0,0 +1,94 @@ +package eu.dnetlib.dhp.datacite + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.AbstractScalaApplication +import eu.dnetlib.dhp.collection.CollectionUtils.fixRelations +import eu.dnetlib.dhp.common.Constants.{MDSTORE_DATA_PATH, MDSTORE_SIZE_PATH} +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup +import eu.dnetlib.dhp.schema.mdstore.{MDStoreVersion, MetadataRecord} +import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.utils.DHPUtils.writeHdfsFile +import eu.dnetlib.dhp.utils.ISLookupClientFactory +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.slf4j.{Logger, LoggerFactory} + + +class GenerateDataciteDatasetSpark (propertyPath:String, args:Array[String], log:Logger) extends AbstractScalaApplication(propertyPath, args, log:Logger) { + /** + * Here all the spark applications runs this method + * where the whole logic of the spark node is defined + */ + override def run(): Unit = { + + val sourcePath = parser.get("sourcePath") + log.info(s"SourcePath is '$sourcePath'") + val exportLinks = "true".equalsIgnoreCase(parser.get("exportLinks")) + log.info(s"exportLinks is '$exportLinks'") + val isLookupUrl: String = parser.get("isLookupUrl") + log.info("isLookupUrl: {}", isLookupUrl) + + val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl) + val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService) + require(vocabularies != null) + + val mdstoreOutputVersion = parser.get("mdstoreOutputVersion") + log.info(s"mdstoreOutputVersion is '$mdstoreOutputVersion'") + + val mapper = new ObjectMapper() + val cleanedMdStoreVersion = mapper.readValue(mdstoreOutputVersion, classOf[MDStoreVersion]) + val outputBasePath = cleanedMdStoreVersion.getHdfsPath + log.info(s"outputBasePath is '$outputBasePath'") + val targetPath = s"$outputBasePath/$MDSTORE_DATA_PATH" + log.info(s"targetPath is '$targetPath'") + + generateDataciteDataset(sourcePath, exportLinks, vocabularies, targetPath, spark) + + reportTotalSize(targetPath, outputBasePath) + } + + + /** + * For working with MDStore we need to store in a file on hdfs the size of + * the current dataset + * @param targetPath + * @param outputBasePath + */ + def reportTotalSize( targetPath: String, outputBasePath: String ):Unit = { + val total_items = spark.read.load(targetPath).count() + writeHdfsFile(spark.sparkContext.hadoopConfiguration, s"$total_items", outputBasePath + MDSTORE_SIZE_PATH) + } + + /** + * Generate the transformed and cleaned OAF Dataset from the native one + + * @param sourcePath sourcePath of the native Dataset in format JSON/Datacite + * @param exportLinks If true it generates unresolved links + * @param vocabularies vocabularies for cleaning + * @param targetPath the targetPath of the result Dataset + */ + def generateDataciteDataset(sourcePath: String, exportLinks: Boolean, vocabularies: VocabularyGroup, targetPath: String, spark:SparkSession):Unit = { + require(spark!= null) + import spark.implicits._ + + implicit val mrEncoder: Encoder[MetadataRecord] = Encoders.kryo[MetadataRecord] + + implicit val resEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + spark.read.load(sourcePath).as[DataciteType] + .filter(d => d.isActive) + .flatMap(d => DataciteToOAFTransformation.generateOAF(d.json, d.timestamp, d.timestamp, vocabularies, exportLinks)) + .filter(d => d != null) + .flatMap(i => fixRelations(i)).filter(i => i != null) + .write.mode(SaveMode.Overwrite).save(targetPath) + } + +} + + +object GenerateDataciteDatasetSpark { + + val log: Logger = LoggerFactory.getLogger(GenerateDataciteDatasetSpark.getClass) + + def main(args: Array[String]): Unit = { + new GenerateDataciteDatasetSpark("/eu/dnetlib/dhp/datacite/generate_dataset_params.json", args, log).initialize().run() + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/ImportDatacite.scala similarity index 93% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/ImportDatacite.scala index 2b73d2955..018b4958a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/ImportDatacite.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/ImportDatacite.scala @@ -1,6 +1,5 @@ -package eu.dnetlib.dhp.actionmanager.datacite +package eu.dnetlib.dhp.datacite -import eu.dnetlib.dhp.actionmanager.datacite.DataciteToOAFTransformation.df_it import eu.dnetlib.dhp.application.ArgumentApplicationParser import org.apache.hadoop.conf.Configuration import org.apache.hadoop.fs.{FileSystem, LocalFileSystem, Path} @@ -9,14 +8,14 @@ import org.apache.hadoop.io.{IntWritable, SequenceFile, Text} import org.apache.spark.SparkContext import org.apache.spark.rdd.RDD import org.apache.spark.sql.expressions.Aggregator +import org.apache.spark.sql.functions.max import org.apache.spark.sql.{Dataset, Encoder, SaveMode, SparkSession} import org.json4s.DefaultFormats import org.json4s.jackson.JsonMethods.parse -import org.apache.spark.sql.functions.max import org.slf4j.{Logger, LoggerFactory} -import java.time.format.DateTimeFormatter._ -import java.time.{LocalDate, LocalDateTime, ZoneOffset} +import java.time.format.DateTimeFormatter.ISO_DATE_TIME +import java.time.{LocalDateTime, ZoneOffset} import scala.io.Source object ImportDatacite { @@ -138,11 +137,11 @@ object ImportDatacite { } } - private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs:Int): Long = { - var from:Long = timestamp * 1000 - val delta:Long = 100000000L + private def writeSequenceFile(hdfsTargetPath: Path, timestamp: Long, conf: Configuration, bs: Int): Long = { + var from: Long = timestamp * 1000 + val delta: Long = 100000000L var client: DataciteAPIImporter = null - val now :Long =System.currentTimeMillis() + val now: Long = System.currentTimeMillis() var i = 0 try { val writer = SequenceFile.createWriter(conf, SequenceFile.Writer.file(hdfsTargetPath), SequenceFile.Writer.keyClass(classOf[IntWritable]), SequenceFile.Writer.valueClass(classOf[Text])) @@ -168,7 +167,7 @@ object ImportDatacite { start = System.currentTimeMillis } } - println(s"updating from value: $from -> ${from+delta}") + println(s"updating from value: $from -> ${from + delta}") from = from + delta } } catch { @@ -183,4 +182,4 @@ object ImportDatacite { i } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/SparkDownloadUpdateDatacite.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala similarity index 68% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/SparkDownloadUpdateDatacite.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala index 0b459fcf6..d46e5423d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/datacite/SparkDownloadUpdateDatacite.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/datacite/SparkDownloadUpdateDatacite.scala @@ -1,18 +1,14 @@ -package eu.dnetlib.dhp.actionmanager.datacite - +package eu.dnetlib.dhp.datacite import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.{Oaf, Result} -import org.apache.hadoop.conf.Configuration -import org.apache.hadoop.fs.LocalFileSystem -import org.apache.hadoop.hdfs.DistributedFileSystem import org.apache.spark.SparkConf -import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.apache.spark.sql.functions.max +import org.apache.spark.sql.{Encoder, Encoders, SparkSession} import org.slf4j.{Logger, LoggerFactory} import java.text.SimpleDateFormat -import java.util.{Date, Locale} +import java.util.Locale import scala.io.Source object SparkDownloadUpdateDatacite { @@ -21,7 +17,7 @@ object SparkDownloadUpdateDatacite { def main(args: Array[String]): Unit = { val conf = new SparkConf - val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json")).mkString) + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/datacite/generate_dataset_params.json")).mkString) parser.parseArgument(args) val master = parser.get("master") val sourcePath = parser.get("sourcePath") @@ -42,9 +38,9 @@ object SparkDownloadUpdateDatacite { import spark.implicits._ - val maxDate:String = spark.read.load(workingPath).as[Oaf].filter(s => s.isInstanceOf[Result]).map(r => r.asInstanceOf[Result].getDateofcollection).select(max("value")).first().getString(0) + val maxDate: String = spark.read.load(workingPath).as[Oaf].filter(s => s.isInstanceOf[Result]).map(r => r.asInstanceOf[Result].getDateofcollection).select(max("value")).first().getString(0) val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US) - val string_to_date =ISO8601FORMAT.parse(maxDate) + val string_to_date = ISO8601FORMAT.parse(maxDate) val ts = string_to_date.getTime diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala similarity index 83% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala index 90b65c8f7..70dcc0184 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/BioDBToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/BioDBToOAF.scala @@ -1,14 +1,12 @@ -package eu.dnetlib.dhp.sx.graph.bio +package eu.dnetlib.dhp.sx.bio import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, OafMapperUtils} -import eu.dnetlib.dhp.schema.oaf.{Author, DataInfo, Dataset, Instance, KeyValue, Oaf, Relation, StructuredProperty} +import eu.dnetlib.dhp.schema.oaf._ import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.{compact, parse, render} - -import scala.collection.JavaConverters._ - +import collection.JavaConverters._ object BioDBToOAF { case class EBILinkItem(id: Long, links: String) {} @@ -17,23 +15,23 @@ object BioDBToOAF { case class UniprotDate(date: String, date_info: String) {} - case class ScholixResolved(pid:String, pidType:String, typology:String, tilte:List[String], datasource:List[String], date:List[String], authors:List[String]){} + case class ScholixResolved(pid: String, pidType: String, typology: String, tilte: List[String], datasource: List[String], date: List[String], authors: List[String]) {} val DATA_INFO: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9") val SUBJ_CLASS = "Keywords" val DATE_RELATION_KEY = "RelationDate" - val resolvedURL:Map[String,String] = Map( - "genbank"-> "https://www.ncbi.nlm.nih.gov/nuccore/", - "ncbi-n" -> "https://www.ncbi.nlm.nih.gov/nuccore/", - "ncbi-wgs" -> "https://www.ncbi.nlm.nih.gov/nuccore/", - "ncbi-p" -> "https://www.ncbi.nlm.nih.gov/protein/", - "ena" -> "https://www.ebi.ac.uk/ena/browser/view/", - "clinicaltrials.gov"-> "https://clinicaltrials.gov/ct2/show/", - "onim"-> "https://omim.org/entry/", - "refseq"-> "https://www.ncbi.nlm.nih.gov/nuccore/", - "geo"-> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" + val resolvedURL: Map[String, String] = Map( + "genbank" -> "https://www.ncbi.nlm.nih.gov/nuccore/", + "ncbi-n" -> "https://www.ncbi.nlm.nih.gov/nuccore/", + "ncbi-wgs" -> "https://www.ncbi.nlm.nih.gov/nuccore/", + "ncbi-p" -> "https://www.ncbi.nlm.nih.gov/protein/", + "ena" -> "https://www.ebi.ac.uk/ena/browser/view/", + "clinicaltrials.gov" -> "https://clinicaltrials.gov/ct2/show/", + "onim" -> "https://omim.org/entry/", + "refseq" -> "https://www.ncbi.nlm.nih.gov/nuccore/", + "geo" -> "https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=" ) @@ -45,7 +43,7 @@ object BioDBToOAF { val ElsevierCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::8f87e10869299a5fe80b315695296b88", "Elsevier") val springerNatureCollectedFrom: KeyValue = OafMapperUtils.keyValue("10|openaire____::6e380d9cf51138baec8480f5a0ce3a2e", "Springer Nature") val EBICollectedFrom: KeyValue = OafMapperUtils.keyValue("10|opendoar____::83e60e09c222f206c725385f53d7e567c", "EMBL-EBIs Protein Data Bank in Europe (PDBe)") - val pubmedCollectedFrom:KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central") + val pubmedCollectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central") UNIPROTCollectedFrom.setDataInfo(DATA_INFO) PDBCollectedFrom.setDataInfo(DATA_INFO) @@ -58,9 +56,9 @@ object BioDBToOAF { Map( "uniprot" -> UNIPROTCollectedFrom, - "pdb"-> PDBCollectedFrom, - "elsevier" ->ElsevierCollectedFrom, - "ebi" ->EBICollectedFrom, + "pdb" -> PDBCollectedFrom, + "elsevier" -> ElsevierCollectedFrom, + "ebi" -> EBICollectedFrom, "Springer Nature" -> springerNatureCollectedFrom, "NCBI Nucleotide" -> ncbiCollectedFrom, "European Nucleotide Archive" -> enaCollectedFrom, @@ -68,7 +66,7 @@ object BioDBToOAF { ) } - def crossrefLinksToOaf(input:String):Oaf = { + def crossrefLinksToOaf(input: String): Oaf = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) val source_pid = (json \ "Source" \ "Identifier" \ "ID").extract[String].toLowerCase @@ -77,16 +75,16 @@ object BioDBToOAF { val target_pid = (json \ "Target" \ "Identifier" \ "ID").extract[String].toLowerCase val target_pid_type = (json \ "Target" \ "Identifier" \ "IDScheme").extract[String].toLowerCase - val relation_semantic= (json \ "RelationshipType" \ "Name").extract[String] + val relation_semantic = (json \ "RelationshipType" \ "Name").extract[String] val date = GraphCleaningFunctions.cleanDate((json \ "LinkedPublicationDate").extract[String]) - createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type),collectedFromMap("elsevier"),"relationship", relation_semantic, date) + createRelation(target_pid, target_pid_type, generate_unresolved_id(source_pid, source_pid_type), collectedFromMap("elsevier"), "relationship", relation_semantic, date) } - def scholixResolvedToOAF(input:ScholixResolved):Oaf = { + def scholixResolvedToOAF(input: ScholixResolved): Oaf = { val d = new Dataset @@ -127,18 +125,18 @@ object BioDBToOAF { d.setInstance(List(i).asJava) if (input.authors != null && input.authors.nonEmpty) { - val authors = input.authors.map(a =>{ + val authors = input.authors.map(a => { val authorOAF = new Author authorOAF.setFullname(a) authorOAF }) d.setAuthor(authors.asJava) } - if (input.date!= null && input.date.nonEmpty) { - val dt = input.date.head - i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO)) - d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO)) - } + if (input.date != null && input.date.nonEmpty) { + val dt = input.date.head + i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO)) + d.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(dt), DATA_INFO)) + } d } @@ -190,7 +188,7 @@ object BioDBToOAF { OafMapperUtils.structuredProperty(s, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, null) ).asJava) } - var i_date:Option[UniprotDate] = None + var i_date: Option[UniprotDate] = None if (dates.nonEmpty) { i_date = dates.find(d => d.date_info.contains("entry version")) @@ -218,12 +216,12 @@ object BioDBToOAF { if (references_pmid != null && references_pmid.nonEmpty) { - val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null) + val rel = createRelation(references_pmid.head, "pmid", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null) rel.getCollectedfrom List(d, rel) } else if (references_doi != null && references_doi.nonEmpty) { - val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null) + val rel = createRelation(references_doi.head, "doi", d.getId, collectedFromMap("uniprot"), ModelConstants.RELATIONSHIP, ModelConstants.IS_RELATED_TO, if (i_date.isDefined) i_date.get.date else null) List(d, rel) } else @@ -231,13 +229,12 @@ object BioDBToOAF { } - - def generate_unresolved_id(pid:String, pidType:String) :String = { + def generate_unresolved_id(pid: String, pidType: String): String = { s"unresolved::$pid::$pidType" } - def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType:String, relClass:String, date:String):Relation = { + def createRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, subRelType: String, relClass: String, date: String): Relation = { val rel = new Relation rel.setCollectedfrom(List(collectedFromMap("pdb")).asJava) @@ -251,7 +248,7 @@ object BioDBToOAF { rel.setTarget(s"unresolved::$pid::$pidType") - val dateProps:KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date) + val dateProps: KeyValue = OafMapperUtils.keyValue(DATE_RELATION_KEY, date) rel.setProperties(List(dateProps).asJava) @@ -262,8 +259,8 @@ object BioDBToOAF { } - def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date:String): Relation = { - createRelation(pid,pidType,sourceId,collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date) + def createSupplementaryRelation(pid: String, pidType: String, sourceId: String, collectedFrom: KeyValue, date: String): Relation = { + createRelation(pid, pidType, sourceId, collectedFrom, ModelConstants.SUPPLEMENT, ModelConstants.IS_SUPPLEMENT_TO, date) } @@ -338,7 +335,7 @@ object BioDBToOAF { def EBITargetLinksFilter(input: EBILinks): Boolean = { - input.targetPidType.equalsIgnoreCase("ena") || input.targetPidType.equalsIgnoreCase("pdb") || input.targetPidType.equalsIgnoreCase("uniprot") + input.targetPidType.equalsIgnoreCase("ena") || input.targetPidType.equalsIgnoreCase("pdb") || input.targetPidType.equalsIgnoreCase("uniprot") } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/SparkTransformBioDatabaseToOAF.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala similarity index 60% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/SparkTransformBioDatabaseToOAF.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala index d66cc84ec..8ae8285e3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/SparkTransformBioDatabaseToOAF.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/SparkTransformBioDatabaseToOAF.scala @@ -1,8 +1,9 @@ -package eu.dnetlib.dhp.sx.graph.bio +package eu.dnetlib.dhp.sx.bio import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Oaf, Result} +import eu.dnetlib.dhp.schema.oaf.Oaf import BioDBToOAF.ScholixResolved +import eu.dnetlib.dhp.collection.CollectionUtils import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} @@ -13,7 +14,7 @@ object SparkTransformBioDatabaseToOAF { def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() val log: Logger = LoggerFactory.getLogger(getClass) - val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/bio_to_oaf_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json"))) parser.parseArgument(args) val database: String = parser.get("database") log.info("database: {}", database) @@ -31,18 +32,17 @@ object SparkTransformBioDatabaseToOAF { .master(parser.get("master")).getOrCreate() val sc = spark.sparkContext - implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) - import spark.implicits._ - + implicit val resultEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) + import spark.implicits._ database.toUpperCase() match { case "UNIPROT" => - spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).write.mode(SaveMode.Overwrite).save(targetPath) - case "PDB"=> - spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath) + spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.uniprotToOAF(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) + case "PDB" => + spark.createDataset(sc.textFile(dbPath).flatMap(i => BioDBToOAF.pdbTOOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) case "SCHOLIX" => - spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).write.mode(SaveMode.Overwrite).save(targetPath) - case "CROSSREF_LINKS"=> - spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).write.mode(SaveMode.Overwrite).save(targetPath) + spark.read.load(dbPath).as[ScholixResolved].map(i => BioDBToOAF.scholixResolvedToOAF(i)).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) + case "CROSSREF_LINKS" => + spark.createDataset(sc.textFile(dbPath).map(i => BioDBToOAF.crossrefLinksToOaf(i))).flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null).write.mode(SaveMode.Overwrite).save(targetPath) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala similarity index 69% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala index ee76cf8ad..17d21f19c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkCreateBaselineDataFrame.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkCreateBaselineDataFrame.scala @@ -1,9 +1,9 @@ -package eu.dnetlib.dhp.sx.graph.ebi +package eu.dnetlib.dhp.sx.bio.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.oaf.Result -import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf} +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal, PMParser, PubMedToOaf} import eu.dnetlib.dhp.utils.ISLookupClientFactory import org.apache.commons.io.IOUtils import org.apache.hadoop.conf.Configuration @@ -24,24 +24,24 @@ import scala.xml.pull.XMLEventReader object SparkCreateBaselineDataFrame { - def requestBaseLineUpdatePage(maxFile:String):List[(String,String)] = { - val data =requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/") + def requestBaseLineUpdatePage(maxFile: String): List[(String, String)] = { + val data = requestPage("https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/") - val result =data.lines.filter(l => l.startsWith("") val start = l.indexOf("= 0 && end >start) - l.substring(start+9, (end-start)) + if (start >= 0 && end > start) + l.substring(start + 9, end - start) else "" - }.filter(s =>s.endsWith(".gz") ).filter(s => s > maxFile).map(s => (s,s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s")).toList + }.filter(s => s.endsWith(".gz")).filter(s => s > maxFile).map(s => (s, s"https://ftp.ncbi.nlm.nih.gov/pubmed/updatefiles/$s")).toList result } - def downloadBaselinePart(url:String):InputStream = { + def downloadBaselinePart(url: String): InputStream = { val r = new HttpGet(url) val timeout = 60; // seconds val config = RequestConfig.custom() @@ -55,7 +55,7 @@ object SparkCreateBaselineDataFrame { } - def requestPage(url:String):String = { + def requestPage(url: String): String = { val r = new HttpGet(url) val timeout = 60; // seconds val config = RequestConfig.custom() @@ -90,25 +90,21 @@ object SparkCreateBaselineDataFrame { } - - - - - def downloadBaseLineUpdate(baselinePath:String, hdfsServerUri:String ):Unit = { + def downloadBaseLineUpdate(baselinePath: String, hdfsServerUri: String): Unit = { val conf = new Configuration conf.set("fs.defaultFS", hdfsServerUri) - val fs = FileSystem.get(conf) + val fs = FileSystem.get(conf) val p = new Path(baselinePath) - val files = fs.listFiles(p,false) + val files = fs.listFiles(p, false) var max_file = "" while (files.hasNext) { val c = files.next() val data = c.getPath.toString - val fileName = data.substring(data.lastIndexOf("/")+1) + val fileName = data.substring(data.lastIndexOf("/") + 1) - if (fileName> max_file) + if (fileName > max_file) max_file = fileName } @@ -118,11 +114,7 @@ object SparkCreateBaselineDataFrame { val hdfsWritePath: Path = new Path(s"$baselinePath/${u._1}") val fsDataOutputStream: FSDataOutputStream = fs.create(hdfsWritePath, true) val i = downloadBaselinePart(u._2) - val buffer = Array.fill[Byte](1024)(0) - while(i.read(buffer)>0) { - fsDataOutputStream.write(buffer) - } - i.close() + IOUtils.copy(i, fsDataOutputStream) println(s"Downloaded ${u._2} into $baselinePath/${u._1}") fsDataOutputStream.close() } @@ -134,11 +126,11 @@ object SparkCreateBaselineDataFrame { override def zero: PMArticle = new PMArticle override def reduce(b: PMArticle, a: (String, PMArticle)): PMArticle = { - if (b != null && b.getPmid!= null) b else a._2 + if (b != null && b.getPmid != null) b else a._2 } override def merge(b1: PMArticle, b2: PMArticle): PMArticle = { - if (b1 != null && b1.getPmid!= null) b1 else b2 + if (b1 != null && b1.getPmid != null) b1 else b2 } @@ -153,7 +145,7 @@ object SparkCreateBaselineDataFrame { def main(args: Array[String]): Unit = { val conf: SparkConf = new SparkConf() val log: Logger = LoggerFactory.getLogger(getClass) - val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(SparkEBILinksToOaf.getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json"))) parser.parseArgument(args) val isLookupUrl: String = parser.get("isLookupUrl") log.info("isLookupUrl: {}", isLookupUrl) @@ -166,6 +158,9 @@ object SparkCreateBaselineDataFrame { val hdfsServerUri = parser.get("hdfsServerUri") log.info("hdfsServerUri: {}", targetPath) + val skipUpdate = parser.get("skipUpdate") + log.info("skipUpdate: {}", skipUpdate) + val isLookupService = ISLookupClientFactory.getLookUpService(isLookupUrl) val vocabularies = VocabularyGroup.loadVocsFromIS(isLookupService) @@ -175,32 +170,31 @@ object SparkCreateBaselineDataFrame { .config(conf) .appName(SparkEBILinksToOaf.getClass.getSimpleName) .master(parser.get("master")).getOrCreate() - import spark.implicits._ val sc = spark.sparkContext + import spark.implicits._ - implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle]) - implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) - implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) - implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle]) + implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) + implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) + implicit val resultEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) - downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri) - - val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline",2000) - val ds:Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i =>{ - val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes())) - new PMParser(xml) - - } )) - - ds.map(p => (p.getPmid,p))(Encoders.tuple(Encoders.STRING, PMEncoder)).groupByKey(_._1) - .agg(pmArticleAggregator.toColumn) - .map(p => p._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset") + if (!"true".equalsIgnoreCase(skipUpdate)) { + downloadBaseLineUpdate(s"$workingPath/baseline", hdfsServerUri) + val k: RDD[(String, String)] = sc.wholeTextFiles(s"$workingPath/baseline", 2000) + val ds: Dataset[PMArticle] = spark.createDataset(k.filter(i => i._1.endsWith(".gz")).flatMap(i => { + val xml = new XMLEventReader(Source.fromBytes(i._2.getBytes())) + new PMParser(xml) + })) + ds.map(p => (p.getPmid, p))(Encoders.tuple(Encoders.STRING, PMEncoder)).groupByKey(_._1) + .agg(pmArticleAggregator.toColumn) + .map(p => p._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/baseline_dataset") + } val exported_dataset = spark.read.load(s"$workingPath/baseline_dataset").as[PMArticle] exported_dataset .map(a => PubMedToOaf.convert(a, vocabularies)).as[Result] - .filter(p => p!= null) + .filter(p => p != null) .write.mode(SaveMode.Overwrite).save(targetPath) } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala similarity index 65% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala index e940fdff0..eab6b1dc6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkDownloadEBILinks.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkDownloadEBILinks.scala @@ -1,8 +1,9 @@ -package eu.dnetlib.dhp.sx.graph.ebi +package eu.dnetlib.dhp.sx.bio.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem -import eu.dnetlib.dhp.sx.graph.bio.pubmed.{PMArticle, PMAuthor, PMJournal} +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMAuthor, PMJournal} +import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem +import eu.dnetlib.dhp.sx.bio.pubmed.PMJournal import org.apache.commons.io.IOUtils import org.apache.http.client.config.RequestConfig import org.apache.http.client.methods.HttpGet @@ -14,15 +15,15 @@ import org.slf4j.{Logger, LoggerFactory} object SparkDownloadEBILinks { - def createEBILinks(pmid:Long):EBILinkItem = { + def createEBILinks(pmid: Long): EBILinkItem = { val res = requestLinks(pmid) - if (res!=null) + if (res != null) return EBILinkItem(pmid, res) null } - def requestPage(url:String):String = { + def requestPage(url: String): String = { val r = new HttpGet(url) val timeout = 60; // seconds val config = RequestConfig.custom() @@ -56,16 +57,17 @@ object SparkDownloadEBILinks { } } - def requestLinks(PMID:Long):String = { + def requestLinks(PMID: Long): String = { requestPage(s"https://www.ebi.ac.uk/europepmc/webservices/rest/MED/$PMID/datalinks?format=json") } + def main(args: Array[String]): Unit = { val log: Logger = LoggerFactory.getLogger(getClass) val MAX_ITEM_PER_PARTITION = 20000 val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_download_update.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession @@ -76,39 +78,39 @@ object SparkDownloadEBILinks { import spark.implicits._ - implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle]) - implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) - implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) + implicit val PMEncoder: Encoder[PMArticle] = Encoders.kryo(classOf[PMArticle]) + implicit val PMJEncoder: Encoder[PMJournal] = Encoders.kryo(classOf[PMJournal]) + implicit val PMAEncoder: Encoder[PMAuthor] = Encoders.kryo(classOf[PMAuthor]) val sourcePath = parser.get("sourcePath") log.info(s"sourcePath -> $sourcePath") val workingPath = parser.get("workingPath") log.info(s"workingPath -> $workingPath") - log.info("Getting max pubmedId where the links have been requested") - val links:Dataset[EBILinkItem] = spark.read.load(s"$sourcePath/ebi_links_dataset").as[EBILinkItem] - val lastPMIDRequested =links.map(l => l.id).select(max("value")).first.getLong(0) + log.info("Getting max pubmedId where the links have already requested") + val links: Dataset[EBILinkItem] = spark.read.load(s"$sourcePath/ebi_links_dataset").as[EBILinkItem] + val lastPMIDRequested = links.map(l => l.id).select(max("value")).first.getLong(0) log.info("Retrieving PMID to request links") val pubmed = spark.read.load(s"$sourcePath/baseline_dataset").as[PMArticle] pubmed.map(p => p.getPmid.toLong).where(s"value > $lastPMIDRequested").write.mode(SaveMode.Overwrite).save(s"$workingPath/id_to_request") - val pmidToReq:Dataset[Long] = spark.read.load(s"$workingPath/id_to_request").as[Long] + val pmidToReq: Dataset[Long] = spark.read.load(s"$workingPath/id_to_request").as[Long] val total = pmidToReq.count() - spark.createDataset(pmidToReq.rdd.repartition((total/MAX_ITEM_PER_PARTITION).toInt).map(pmid =>createEBILinks(pmid)).filter(l => l!= null)).write.mode(SaveMode.Overwrite).save(s"$workingPath/links_update") + spark.createDataset(pmidToReq.rdd.repartition((total / MAX_ITEM_PER_PARTITION).toInt).map(pmid => createEBILinks(pmid)).filter(l => l != null)).write.mode(SaveMode.Overwrite).save(s"$workingPath/links_update") - val updates:Dataset[EBILinkItem] =spark.read.load(s"$workingPath/links_update").as[EBILinkItem] + val updates: Dataset[EBILinkItem] = spark.read.load(s"$workingPath/links_update").as[EBILinkItem] links.union(updates).groupByKey(_.id) - .reduceGroups{(x,y) => - if (x == null || x.links ==null) + .reduceGroups { (x, y) => + if (x == null || x.links == null) y - if (y ==null || y.links ==null) + if (y == null || y.links == null) x if (x.links.length > y.links.length) - x + x else y }.map(_._2).write.mode(SaveMode.Overwrite).save(s"$workingPath/links_final") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkEBILinksToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala similarity index 61% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkEBILinksToOaf.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala index 1924d919e..8da617ca0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/ebi/SparkEBILinksToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/ebi/SparkEBILinksToOaf.scala @@ -1,21 +1,22 @@ -package eu.dnetlib.dhp.sx.graph.ebi +package eu.dnetlib.dhp.sx.bio.ebi import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.schema.oaf.Oaf -import eu.dnetlib.dhp.sx.graph.bio -import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF -import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.EBILinkItem +import eu.dnetlib.dhp.sx.bio.BioDBToOAF +import eu.dnetlib.dhp.sx.bio.BioDBToOAF.EBILinkItem +import BioDBToOAF.EBILinkItem +import eu.dnetlib.dhp.collection.CollectionUtils import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf -import org.apache.spark.rdd.RDD -import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.apache.spark.sql._ import org.slf4j.{Logger, LoggerFactory} + object SparkEBILinksToOaf { def main(args: Array[String]): Unit = { val log: Logger = LoggerFactory.getLogger(getClass) val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/ebi/ebi_to_df_params.json"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession @@ -24,19 +25,20 @@ object SparkEBILinksToOaf { .appName(SparkEBILinksToOaf.getClass.getSimpleName) .master(parser.get("master")).getOrCreate() + + import spark.implicits._ val sourcePath = parser.get("sourcePath") log.info(s"sourcePath -> $sourcePath") val targetPath = parser.get("targetPath") log.info(s"targetPath -> $targetPath") + implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) - import spark.implicits._ - implicit val PMEncoder: Encoder[Oaf] = Encoders.kryo(classOf[Oaf]) + val ebLinks: Dataset[EBILinkItem] = spark.read.load(sourcePath).as[EBILinkItem].filter(l => l.links != null && l.links.startsWith("{")) - val ebLinks:Dataset[EBILinkItem] = spark.read.load(s"${sourcePath}_dataset").as[EBILinkItem].filter(l => l.links!= null) - - ebLinks.flatMap(j =>BioDBToOAF.parse_ebi_links(j.links)) + ebLinks.flatMap(j => BioDBToOAF.parse_ebi_links(j.links)) .filter(p => BioDBToOAF.EBITargetLinksFilter(p)) .flatMap(p => BioDBToOAF.convertEBILinksToOaf(p)) + .flatMap(i=> CollectionUtils.fixRelations(i)).filter(i => i != null) .write.mode(SaveMode.Overwrite).save(targetPath) } } diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java new file mode 100644 index 000000000..af0d5169d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMArticle.java @@ -0,0 +1,253 @@ + +package eu.dnetlib.dhp.sx.bio.pubmed; + +import java.io.Serializable; +import java.util.ArrayList; +import java.util.List; + +/** + * This class represent an instance of Pubmed Article extracted from the native XML + * + * @author Sandro La Bruzzo + */ + +public class PMArticle implements Serializable { + + /** + * the Pubmed Identifier + */ + private String pmid; + /** + * the DOI + */ + private String doi; + /** + * the Pubmed Date extracted from Specifies a date significant to either the article's history or the citation's processing. + * All dates will have a , , and elements. Some may have an , , and element(s). + */ + private String date; + /** + * This is an 'envelop' element that contains various elements describing the journal cited; i.e., ISSN, Volume, Issue, and PubDate and author name(s), however, it does not contain data itself. + */ + private PMJournal journal; + /** + * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. The NLM journal title abbreviation is exported in the element. + */ + private String title; + /** + * English-language abstracts are taken directly from the published article. + * If the article does not have a published abstract, the National Library of Medicine does not create one, + * thus the record lacks the and elements. However, in the absence of a formally + * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. + */ + private String description; + /** + * the language in which an article was published is recorded in . + * All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single + * record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value. + * Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined. + */ + private String language; + + /** + * NLM controlled vocabulary, Medical Subject Headings (MeSH®), is used to characterize the content of the articles represented by MEDLINE citations. * + */ + private final List subjects = new ArrayList<>(); + /** + * This element is used to identify the type of article indexed for MEDLINE; + * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of + * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural). + */ + private final List publicationTypes = new ArrayList<>(); + /** + * Personal and collective (corporate) author names published with the article are found in . + */ + private List authors = new ArrayList<>(); + + /** + * contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service + * or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations. + */ + private final List grants = new ArrayList<>(); + + /** + * get the DOI + * @return a DOI + */ + public String getDoi() { + return doi; + } + + /** + * Set the DOI + * @param doi a DOI + */ + public void setDoi(String doi) { + this.doi = doi; + } + + /** + * get the Pubmed Identifier + * @return the PMID + */ + public String getPmid() { + return pmid; + } + + /** + * set the Pubmed Identifier + * @param pmid the Pubmed Identifier + */ + public void setPmid(String pmid) { + this.pmid = pmid; + } + + /** + * the Pubmed Date extracted from Specifies a date significant to either the article's history or the citation's processing. + * All dates will have a , , and elements. Some may have an , , and element(s). + * + * @return the Pubmed Date + */ + public String getDate() { + return date; + } + + /** + * Set the pubmed Date + * @param date + */ + public void setDate(String date) { + this.date = date; + } + + /** + * The full journal title (taken from NLM cataloging data following NLM rules for how to compile a serial name) is exported in this element. + * Some characters that are not part of the NLM MEDLINE/PubMed Character Set reside in a relatively small number of full journal titles. + * The NLM journal title abbreviation is exported in the element. + * + * @return the pubmed Journal Extracted + */ + public PMJournal getJournal() { + return journal; + } + + /** + * Set the mapped pubmed Journal + * @param journal + */ + public void setJournal(PMJournal journal) { + this.journal = journal; + } + + /** + * English-language abstracts are taken directly from the published article. + * If the article does not have a published abstract, the National Library of Medicine does not create one, + * thus the record lacks the and elements. However, in the absence of a formally + * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. + * + * @return the extracted pubmed Title + */ + public String getTitle() { + return title; + } + + /** + * set the pubmed title + * @param title + */ + public void setTitle(String title) { + this.title = title; + } + + /** + * English-language abstracts are taken directly from the published article. + * If the article does not have a published abstract, the National Library of Medicine does not create one, + * thus the record lacks the and elements. However, in the absence of a formally + * labeled abstract in the published article, text from a substantive "summary", "summary and conclusions" or "conclusions and summary" may be used. + * + * @return the Mapped Pubmed Article Abstracts + */ + public String getDescription() { + return description; + } + + /** + * Set the Mapped Pubmed Article Abstracts + * @param description + */ + public void setDescription(String description) { + this.description = description; + } + + /** + * Personal and collective (corporate) author names published with the article are found in . + * + * @return get the Mapped Authors lists + */ + public List getAuthors() { + return authors; + } + + /** + * Set the Mapped Authors lists + * @param authors + */ + public void setAuthors(List authors) { + this.authors = authors; + } + + /** + * This element is used to identify the type of article indexed for MEDLINE; + * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of + * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural). + * + * @return the mapped Subjects + */ + public List getSubjects() { + return subjects; + } + + /** + * + * the language in which an article was published is recorded in . + * All entries are three letter abbreviations stored in lower case, such as eng, fre, ger, jpn, etc. When a single + * record contains more than one language value the XML export program extracts the languages in alphabetic order by the 3-letter language value. + * Some records provided by collaborating data producers may contain the value und to identify articles whose language is undetermined. + * + * @return The mapped Language + */ + public String getLanguage() { + return language; + } + + /** + * + * Set The mapped Language + * + * @param language the mapped Language + */ + public void setLanguage(String language) { + this.language = language; + } + + /** + * This element is used to identify the type of article indexed for MEDLINE; + * it characterizes the nature of the information or the manner in which it is conveyed as well as the type of + * research support received (e.g., Review, Letter, Retracted Publication, Clinical Conference, Research Support, N.I.H., Extramural). + * + * @return the mapped Publication Type + */ + public List getPublicationTypes() { + return publicationTypes; + } + + /** + * contains the research grant or contract number (or both) that designates financial support by any agency of the United States Public Health Service + * or any institute of the National Institutes of Health. Additionally, beginning in late 2005, grant numbers are included for many other US and non-US funding agencies and organizations. + * @return the mapped grants + */ + + public List getGrants() { + return grants; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMAuthor.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java similarity index 57% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMAuthor.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java index ba69998c5..68ef6459e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMAuthor.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMAuthor.java @@ -1,29 +1,59 @@ -package eu.dnetlib.dhp.sx.graph.bio.pubmed; +package eu.dnetlib.dhp.sx.bio.pubmed; import java.io.Serializable; +/** + * The type Pubmed author. + * + * @author Sandro La Bruzzo + */ public class PMAuthor implements Serializable { private String lastName; private String foreName; + /** + * Gets last name. + * + * @return the last name + */ public String getLastName() { return lastName; } + /** + * Sets last name. + * + * @param lastName the last name + */ public void setLastName(String lastName) { this.lastName = lastName; } + /** + * Gets fore name. + * + * @return the fore name + */ public String getForeName() { return foreName; } + /** + * Sets fore name. + * + * @param foreName the fore name + */ public void setForeName(String foreName) { this.foreName = foreName; } + /** + * Gets full name. + * + * @return the full name + */ public String getFullName() { return String .format("%s, %s", this.foreName != null ? this.foreName : "", this.lastName != null ? this.lastName : ""); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMGrant.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMGrant.java new file mode 100644 index 000000000..abb908483 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMGrant.java @@ -0,0 +1,87 @@ + +package eu.dnetlib.dhp.sx.bio.pubmed; + +/** + * The type Pm grant. + * + * @author Sandro La Bruzzo + */ +public class PMGrant { + + private String grantID; + private String agency; + private String country; + + /** + * Instantiates a new Pm grant. + */ + public PMGrant() { + } + + /** + * Instantiates a new Pm grant. + * + * @param grantID the grant id + * @param agency the agency + * @param country the country + */ + public PMGrant(String grantID, String agency, String country) { + this.grantID = grantID; + this.agency = agency; + this.country = country; + } + + /** + * Gets grant id. + * + * @return the grant id + */ + public String getGrantID() { + return grantID; + } + + /** + * Sets grant id. + * + * @param grantID the grant id + */ + public void setGrantID(String grantID) { + this.grantID = grantID; + } + + /** + * Gets agency. + * + * @return the agency + */ + public String getAgency() { + return agency; + } + + /** + * Sets agency. + * + * @param agency the agency + */ + public void setAgency(String agency) { + this.agency = agency; + } + + /** + * Gets country. + * + * @return the country + */ + public String getCountry() { + return country; + } + + /** + * Sets country. + * + * @param country the country + */ + public void setCountry(String country) { + this.country = country; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMJournal.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMJournal.java similarity index 53% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMJournal.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMJournal.java index d251354d4..731648839 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMJournal.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMJournal.java @@ -1,8 +1,13 @@ -package eu.dnetlib.dhp.sx.graph.bio.pubmed; +package eu.dnetlib.dhp.sx.bio.pubmed; import java.io.Serializable; +/** + * The type Pm journal. + * + * @author Sandro La Bruzzo + */ public class PMJournal implements Serializable { private String issn; @@ -11,42 +16,92 @@ public class PMJournal implements Serializable { private String date; private String title; + /** + * Gets issn. + * + * @return the issn + */ public String getIssn() { return issn; } + /** + * Sets issn. + * + * @param issn the issn + */ public void setIssn(String issn) { this.issn = issn; } + /** + * Gets volume. + * + * @return the volume + */ public String getVolume() { return volume; } + /** + * Sets volume. + * + * @param volume the volume + */ public void setVolume(String volume) { this.volume = volume; } + /** + * Gets issue. + * + * @return the issue + */ public String getIssue() { return issue; } + /** + * Sets issue. + * + * @param issue the issue + */ public void setIssue(String issue) { this.issue = issue; } + /** + * Gets date. + * + * @return the date + */ public String getDate() { return date; } + /** + * Sets date. + * + * @param date the date + */ public void setDate(String date) { this.date = date; } + /** + * Gets title. + * + * @return the title + */ public String getTitle() { return title; } + /** + * Sets title. + * + * @param title the title + */ public void setTitle(String title) { this.title = title; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMParser.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala similarity index 98% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMParser.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala index 8744bdfb4..c6d5fdf74 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMParser.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMParser.scala @@ -1,7 +1,13 @@ -package eu.dnetlib.dhp.sx.graph.bio.pubmed +package eu.dnetlib.dhp.sx.bio.pubmed import scala.xml.MetaData import scala.xml.pull.{EvElemEnd, EvElemStart, EvText, XMLEventReader} + + +/** + * + * @param xml + */ class PMParser(xml:XMLEventReader) extends Iterator[PMArticle] { var currentArticle:PMArticle = generateNextArticle() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMSubject.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMSubject.java similarity index 50% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMSubject.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMSubject.java index 354b2cbe5..e3829bb7b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMSubject.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PMSubject.java @@ -1,40 +1,83 @@ -package eu.dnetlib.dhp.sx.graph.bio.pubmed; +package eu.dnetlib.dhp.sx.bio.pubmed; +/** + * The type Pubmed subject. + */ public class PMSubject { private String value; private String meshId; private String registryNumber; + /** + * Instantiates a new Pm subject. + */ public PMSubject() { } + /** + * Instantiates a new Pm subject. + * + * @param value the value + * @param meshId the mesh id + * @param registryNumber the registry number + */ public PMSubject(String value, String meshId, String registryNumber) { this.value = value; this.meshId = meshId; this.registryNumber = registryNumber; } + /** + * Gets value. + * + * @return the value + */ public String getValue() { return value; } + /** + * Sets value. + * + * @param value the value + */ public void setValue(String value) { this.value = value; } + /** + * Gets mesh id. + * + * @return the mesh id + */ public String getMeshId() { return meshId; } + /** + * Sets mesh id. + * + * @param meshId the mesh id + */ public void setMeshId(String meshId) { this.meshId = meshId; } + /** + * Gets registry number. + * + * @return the registry number + */ public String getRegistryNumber() { return registryNumber; } + /** + * Sets registry number. + * + * @param registryNumber the registry number + */ public void setRegistryNumber(String registryNumber) { this.registryNumber = registryNumber; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala similarity index 63% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala index 202eb7b14..ecef32202 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PubMedToOaf.scala +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/sx/bio/pubmed/PubMedToOaf.scala @@ -1,12 +1,16 @@ -package eu.dnetlib.dhp.sx.graph.bio.pubmed +package eu.dnetlib.dhp.sx.bio.pubmed + import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup import eu.dnetlib.dhp.schema.common.ModelConstants -import eu.dnetlib.dhp.schema.oaf._ import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils, PidType} - -import java.util.regex.Pattern +import eu.dnetlib.dhp.schema.oaf._ import scala.collection.JavaConverters._ +import java.util.regex.Pattern + +/** + * + */ object PubMedToOaf { val SUBJ_CLASS = "keywords" @@ -14,8 +18,18 @@ object PubMedToOaf { "pmid" -> "https://pubmed.ncbi.nlm.nih.gov/", "doi" -> "https://dx.doi.org/" ) + val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9") + val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central") - def cleanDoi(doi:String):String = { + + + /** + * Cleaning the DOI Applying regex in order to + * remove doi starting with URL + * @param doi input DOI + * @return cleaned DOI + */ + def cleanDoi(doi: String): String = { val regex = "^10.\\d{4,9}\\/[\\[\\]\\-\\<\\>._;()\\/:A-Z0-9]+$" @@ -29,6 +43,15 @@ object PubMedToOaf { null } + /** + * + * Create an instance of class extends Result + * starting from OAF instanceType value + * + * @param cobjQualifier OAF instance type + * @param vocabularies All dnet vocabularies + * @return the correct instance + */ def createResult(cobjQualifier: Qualifier, vocabularies: VocabularyGroup): Result = { val result_typologies = getVocabularyTerm(ModelConstants.DNET_RESULT_TYPOLOGIES, vocabularies, cobjQualifier.getClassid) result_typologies.getClassid match { @@ -41,6 +64,12 @@ object PubMedToOaf { } } + /** + * Mapping the Pubmedjournal info into the OAF Journale + * + * @param j the pubmedJournal + * @return the OAF Journal + */ def mapJournal(j: PMJournal): Journal = { if (j == null) return null @@ -48,6 +77,7 @@ object PubMedToOaf { journal.setDataInfo(dataInfo) journal.setName(j.getTitle) + journal.setConferencedate(j.getDate) journal.setVol(j.getVolume) journal.setIssnPrinted(j.getIssn) journal.setIss(j.getIssue) @@ -56,69 +86,108 @@ object PubMedToOaf { } - + /** + * + * Find vocabulary term into synonyms and term in the vocabulary + * + * @param vocabularyName the input vocabulary name + * @param vocabularies all the vocabularies + * @param term the term to find + * + * @return the cleaned term value + */ def getVocabularyTerm(vocabularyName: String, vocabularies: VocabularyGroup, term: String): Qualifier = { val a = vocabularies.getSynonymAsQualifier(vocabularyName, term) val b = vocabularies.getTermAsQualifier(vocabularyName, term) if (a == null) b else a } - val dataInfo: DataInfo = OafMapperUtils.dataInfo(false, null, false, false, ModelConstants.PROVENANCE_ACTION_SET_QUALIFIER, "0.9") - val collectedFrom: KeyValue = OafMapperUtils.keyValue(ModelConstants.EUROPE_PUBMED_CENTRAL_ID, "Europe PubMed Central") + /** + * Map the Pubmed Article into the OAF instance + * + * + * @param article the pubmed articles + * @param vocabularies the vocabularies + * @return The OAF instance if the mapping did not fail + */ def convert(article: PMArticle, vocabularies: VocabularyGroup): Result = { if (article.getPublicationTypes == null) return null - val i = new Instance - var pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo)) + + + // MAP PMID into pid with classid = classname = pmid + val pidList: List[StructuredProperty] = List(OafMapperUtils.structuredProperty(article.getPmid, PidType.pmid.toString, PidType.pmid.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo)) if (pidList == null) return null - var alternateIdentifier :StructuredProperty = null + // MAP //ArticleId[./@IdType="doi"] into alternateIdentifier with classid = classname = doi + var alternateIdentifier: StructuredProperty = null if (article.getDoi != null) { val normalizedPid = cleanDoi(article.getDoi) - if (normalizedPid!= null) + if (normalizedPid != null) alternateIdentifier = OafMapperUtils.structuredProperty(normalizedPid, PidType.doi.toString, PidType.doi.toString, ModelConstants.DNET_PID_TYPES, ModelConstants.DNET_PID_TYPES, dataInfo) } + // INSTANCE MAPPING + //-------------------------------------------------------------------------------------- + // If the article contains the typology Journal Article then we apply this type //else We have to find a terms that match the vocabulary otherwise we discard it val ja = article.getPublicationTypes.asScala.find(s => "Journal Article".equalsIgnoreCase(s.getValue)) + val pubmedInstance = new Instance if (ja.isDefined) { val cojbCategory = getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, ja.get.getValue) - i.setInstancetype(cojbCategory) + pubmedInstance.setInstancetype(cojbCategory) } else { val i_type = article.getPublicationTypes.asScala .map(s => getVocabularyTerm(ModelConstants.DNET_PUBLICATION_RESOURCE, vocabularies, s.getValue)) .find(q => q != null) if (i_type.isDefined) - i.setInstancetype(i_type.get) + pubmedInstance.setInstancetype(i_type.get) else return null } - val result = createResult(i.getInstancetype, vocabularies) + val result = createResult(pubmedInstance.getInstancetype, vocabularies) if (result == null) return result result.setDataInfo(dataInfo) - i.setPid(pidList.asJava) - if (alternateIdentifier!= null) - i.setAlternateIdentifier(List(alternateIdentifier).asJava) - result.setInstance(List(i).asJava) - i.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection breakOut) + pubmedInstance.setPid(pidList.asJava) + if (alternateIdentifier != null) + pubmedInstance.setAlternateIdentifier(List(alternateIdentifier).asJava) + result.setInstance(List(pubmedInstance).asJava) + pubmedInstance.getPid.asScala.filter(p => "pmid".equalsIgnoreCase(p.getQualifier.getClassid)).map(p => p.getValue)(collection.breakOut) + //CREATE URL From pmid val urlLists: List[String] = pidList .map(s => (urlMap.getOrElse(s.getQualifier.getClassid, ""), s.getValue)) .filter(t => t._1.nonEmpty) .map(t => t._1 + t._2) if (urlLists != null) - i.setUrl(urlLists.asJava) - i.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo)) - i.setCollectedfrom(collectedFrom) + pubmedInstance.setUrl(urlLists.asJava) + + //ASSIGN DateofAcceptance + pubmedInstance.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo)) + //ASSIGN COLLECTEDFROM + pubmedInstance.setCollectedfrom(collectedFrom) result.setPid(pidList.asJava) + + //END INSTANCE MAPPING + //-------------------------------------------------------------------------------------- + + + // JOURNAL MAPPING + //-------------------------------------------------------------------------------------- if (article.getJournal != null && result.isInstanceOf[Publication]) result.asInstanceOf[Publication].setJournal(mapJournal(article.getJournal)) result.setCollectedfrom(List(collectedFrom).asJava) + //END JOURNAL MAPPING + //-------------------------------------------------------------------------------------- + + + // RESULT MAPPING + //-------------------------------------------------------------------------------------- result.setDateofacceptance(OafMapperUtils.field(GraphCleaningFunctions.cleanDate(article.getDate), dataInfo)) if (article.getTitle == null || article.getTitle.isEmpty) @@ -136,7 +205,7 @@ object PubMedToOaf { } - val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection breakOut) + val subjects: List[StructuredProperty] = article.getSubjects.asScala.map(s => OafMapperUtils.structuredProperty(s.getValue, SUBJ_CLASS, SUBJ_CLASS, ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES, dataInfo))(collection.breakOut) if (subjects != null) result.setSubject(subjects.asJava) @@ -148,7 +217,7 @@ object PubMedToOaf { author.setFullname(a.getFullName) author.setRank(index + 1) author - }(collection breakOut) + }(collection.breakOut) if (authors != null && authors.nonEmpty) @@ -158,6 +227,9 @@ object PubMedToOaf { result.setId(article.getPmid) + + // END RESULT MAPPING + //-------------------------------------------------------------------------------------- val id = IdentifierFactory.createIdentifier(result) if (article.getPmid.equalsIgnoreCase(id)) return null diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json new file mode 100644 index 000000000..050a25677 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/get_fos_parameters.json @@ -0,0 +1,33 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName":"out", + "paramLongName":"outputPath", + "paramDescription": "the output path", + "paramRequired": true + }, + + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "hnn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the path used to store the HostedByMap", + "paramRequired": true + }, + { + "paramName": "cfn", + "paramLongName": "classForName", + "paramDescription": "the path used to store the HostedByMap", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml new file mode 100644 index 000000000..d53504fe6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/oozie_app/workflow.xml @@ -0,0 +1,174 @@ + + + + + fosPath + the input path of the resources to be extended + + + + bipScorePath + the path where to find the bipFinder scores + + + outputPath + the path where to store the actionset + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + yarn + cluster + Produces the unresolved from bip finder! + eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareBipFinder + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${bipScorePath} + --outputPath${workingDir}/prepared + + + + + + + + eu.dnetlib.dhp.actionmanager.createunresolvedentities.GetFOSData + --hdfsNameNode${nameNode} + --sourcePath${fosPath} + --outputPath${workingDir}/input/fos + --classForNameeu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel + + + + + + + + yarn + cluster + Produces the unresolved from FOS! + eu.dnetlib.dhp.actionmanager.createunresolvedentities.PrepareFOSSparkJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/input/fos + --outputPath${workingDir}/prepared + + + + + + + + + + + + + yarn + cluster + Saves the result produced for bip and fos by grouping results with the same id + eu.dnetlib.dhp.actionmanager.createunresolvedentities.SparkSaveUnresolved + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/prepared + --outputPath${outputPath} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json new file mode 100644 index 000000000..b7bad73e6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/prepare_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "sp", + "paramLongName": "sourcePath", + "paramDescription": "the URL from where to get the programme file", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/produce_unresolved_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/produce_unresolved_parameters.json new file mode 100644 index 000000000..b7bad73e6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/produce_unresolved_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "sp", + "paramLongName": "sourcePath", + "paramDescription": "the URL from where to get the programme file", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml deleted file mode 100644 index 69fc95957..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/workflow.xml +++ /dev/null @@ -1,95 +0,0 @@ - - - - mainPath - the working path of Datacite stores - - - oafTargetPath - the target path where the OAF records are stored - - - isLookupUrl - The IS lookUp service endopoint - - - blocksize - 100 - The request block size - - - exportLinks - false - instructs the transformation phase to produce the links or not - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - ${wf:conf('resumeFrom') eq 'TransformDatacite'} - - - - - - - yarn-cluster - cluster - ImportDatacite - eu.dnetlib.dhp.actionmanager.datacite.ImportDatacite - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --targetPath${mainPath}/datacite_update - --dataciteDumpPath${mainPath}/datacite_dump - --namenode${nameNode} - --masteryarn-cluster - --blocksize${blocksize} - - - - - - - - yarn-cluster - cluster - TransformJob - eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${mainPath}/datacite_dump - --targetPath${oafTargetPath} - --isLookupUrl${isLookupUrl} - --exportLinks${exportLinks} - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/workflow.xml deleted file mode 100644 index 397288c69..000000000 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/workflow.xml +++ /dev/null @@ -1,84 +0,0 @@ - - - - datacitePath - the path of Datacite spark dataset - - - isLookupUrl - The IS lookUp service endopoint - - - crossrefPath - the path of Crossref spark dataset - - - - targetPath - the path of Crossref spark dataset - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - yarn-cluster - cluster - ImportDatacite - eu.dnetlib.dhp.actionmanager.datacite.GenerateDataciteDatasetSpark - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${datacitePath} - --targetPath${targetPath}/datacite_oaf - --isLookupUrl${isLookupUrl} - --exportLinkstrue - --masteryarn-cluster - - - - - - - - - yarn-cluster - cluster - FilterCrossrefEntities - eu.dnetlib.dhp.actionmanager.datacite.FilterCrossrefEntitiesSpark - dhp-aggregation-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${crossrefPath} - --targetPath${targetPath}/crossref_oaf - --masteryarn-cluster - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json new file mode 100644 index 000000000..308e02026 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/as_parameters.json @@ -0,0 +1,25 @@ +[ + { + "paramName": "ip", + "paramLongName": "inputPath", + "paramDescription": "the zipped opencitations file", + "paramRequired": true + }, + { + "paramName": "op", + "paramLongName": "outputPath", + "paramDescription": "the working path", + "paramRequired": true + }, + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "the hdfs name node", + "paramRequired": false + }, { + "paramName": "sdr", + "paramLongName": "shouldDuplicateRels", + "paramDescription": "the hdfs name node", + "paramRequired": false +} +] diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json new file mode 100644 index 000000000..4910ad11d --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/input_parameters.json @@ -0,0 +1,20 @@ +[ + { + "paramName": "if", + "paramLongName": "inputFile", + "paramDescription": "the zipped opencitations file", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the working path", + "paramRequired": true + }, + { + "paramName": "hnn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the hdfs name node", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/config-default.xml similarity index 58% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/config-default.xml index 17cd6c9a3..a1755f329 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/config-default.xml @@ -1,7 +1,4 @@ - - - jobTracker yarnRM @@ -10,41 +7,6 @@ nameNode hdfs://nameservice1 - - hive_metastore_uris - thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 - - - spark2YarnHistoryServerAddress - http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 - - - - - - - - - - - - - - - - - - - - - - - - - oozie.launcher.mapreduce.user.classpath.first - true - - oozie.use.system.libpath true @@ -53,16 +15,44 @@ oozie.action.sharelib.for.spark spark2 + + hive_metastore_uris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + spark2YarnHistoryServerAddress + http://iis-cdh5-test-gw.ocean.icm.edu.pl:18089 + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + + + oozie.launcher.mapreduce.user.classpath.first + true + + + sparkExecutorNumber + 4 + spark2EventLogDir /user/spark/spark2ApplicationHistory - spark2ExtraListeners - "com.cloudera.spark.lineage.NavigatorAppListener" + sparkDriverMemory + 15G - spark2SqlQueryExecutionListeners - "com.cloudera.spark.lineage.NavigatorQueryListener" + sparkExecutorMemory + 6G + + + sparkExecutorCores + 1 \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/download.sh b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/download.sh new file mode 100644 index 000000000..7a34f3c4e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/download.sh @@ -0,0 +1,2 @@ +#!/bin/bash +for file in $(echo $1 | tr ";" "\n"); do curl -L $(echo $file | cut -d '@' -f 1 ) | hdfs dfs -put - $2/$(echo $file | cut -d '@' -f 2) ; done; \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml new file mode 100644 index 000000000..d052791a3 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/oozie_app/workflow.xml @@ -0,0 +1,91 @@ + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + + ${wf:conf('resumeFrom') eq 'DownloadDump'} + ${wf:conf('resumeFrom') eq 'ExtractContent'} + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + ${jobTracker} + ${nameNode} + + + mapred.job.queue.name + ${queueName} + + + download.sh + ${filelist} + ${workingPath}/Original + HADOOP_USER_NAME=${wf:user()} + download.sh + + + + + + + + eu.dnetlib.dhp.actionmanager.opencitations.GetOpenCitationsRefs + --hdfsNameNode${nameNode} + --inputFile${inputFile} + --workingPath${workingPath} + + + + + + + + yarn + cluster + Produces the AS for OC + eu.dnetlib.dhp.actionmanager.opencitations.CreateActionSetSparkJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --inputPath${workingPath}/COCI + --outputPath${outputPath} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/opencitations_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/opencitations_parameters.json new file mode 100644 index 000000000..258d6816e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/opencitations/opencitations_parameters.json @@ -0,0 +1,8 @@ +[ + {"paramName":"n", "paramLongName":"hdfsServerUri", "paramDescription": "the server uri", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the default work path", "paramRequired": true}, + {"paramName":"f", "paramLongName":"opencitationFile", "paramDescription": "the name of the file", "paramRequired": true}, + {"paramName":"issm", "paramLongName":"isSparkSessionManaged", "paramDescription": "the name of the activities orcid file", "paramRequired": false}, + {"paramName":"o", "paramLongName":"outputPath", "paramDescription": "the name of the activities orcid file", "paramRequired": true} + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/workflow.xml similarity index 59% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/workflow.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/workflow.xml index 3c58ace7b..6989eed66 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/actionset/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/collection/oozie_app/workflow.xml @@ -1,46 +1,52 @@ - + - sourcePath + mainPath the working path of Datacite stores - outputPath - the path of Datacite ActionSet + isLookupUrl + The IS lookUp service endopoint + + blocksize + 100 + The request block size + + - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + yarn-cluster cluster - ExportDataset - eu.dnetlib.dhp.actionmanager.datacite.ExportActionSetJobNode + ImportDatacite + eu.dnetlib.dhp.datacite.ImportDatacite dhp-aggregation-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=3840 --conf spark.extraListeners=${spark2ExtraListeners} --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --sourcePath${sourcePath} - --targetPath${outputPath} + --targetPath${mainPath}/datacite_update + --dataciteDumpPath${mainPath}/datacite_dump + --namenode${nameNode} --masteryarn-cluster + --blocksize${blocksize} - \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/datacite_filter similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/datacite_filter rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/datacite_filter diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/exportDataset_parameters.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/exportDataset_parameters.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/exportDataset_parameters.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/filter_crossref_param.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/filter_crossref_param.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/filter_crossref_param.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/filter_crossref_param.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/generate_dataset_params.json similarity index 90% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/generate_dataset_params.json index 67e7f37dc..04dc8b942 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/generate_dataset_params.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/generate_dataset_params.json @@ -7,8 +7,8 @@ }, { - "paramName": "t", - "paramLongName": "targetPath", + "paramName": "mo", + "paramLongName": "mdstoreOutputVersion", "paramDescription": "the target mdstore path", "paramRequired": true }, diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/hostedBy_map.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/hostedBy_map.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/import_from_api.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/import_from_api.json similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/import_from_api.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/import_from_api.json diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/workflow.xml new file mode 100644 index 000000000..d5bae7305 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/datacite/transformation/oozie_app/workflow.xml @@ -0,0 +1,126 @@ + + + + mainPath + the working path of Datacite stores + + + isLookupUrl + The IS lookUp service endopoint + + + mdStoreOutputId + the identifier of the cleaned MDStore + + + mdStoreManagerURI + the path of the cleaned mdstore + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionNEW_VERSION + --mdStoreID${mdStoreOutputId} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + + + yarn-cluster + cluster + TransformJob + eu.dnetlib.dhp.datacite.GenerateDataciteDatasetSpark + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=3840 + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${mainPath}/datacite_dump + --mdstoreOutputVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --isLookupUrl${isLookupUrl} + --exportLinkstrue + --masteryarn-cluster + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionCOMMIT + --namenode${nameNode} + --mdStoreVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionREAD_UNLOCK + --mdStoreManagerURI${mdStoreManagerURI} + --readMDStoreId${wf:actionData('BeginRead')['mdStoreReadLockVersion']} + + + + + + + + + + + oozie.launcher.mapreduce.user.classpath.first + true + + + eu.dnetlib.dhp.aggregation.mdstore.MDStoreActionNode + --actionROLLBACK + --mdStoreVersion${wf:actionData('StartTransaction')['mdStoreVersion']} + --mdStoreManagerURI${mdStoreManagerURI} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml new file mode 100644 index 000000000..071d202b6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/db/oozie_app/workflow.xml @@ -0,0 +1,51 @@ + + + + sourcePath + the PDB Database Working Path + + + database + the PDB Database Working Path + + + + targetPath + the Target Working dir path + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Convert Bio DB to OAF Dataset + eu.dnetlib.dhp.sx.bio.SparkTransformBioDatabaseToOAF + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --dbPath${sourcePath} + --database${database} + --targetPath${targetPath} + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json similarity index 83% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json index 4bee770bd..8dc8a2aae 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/baseline_to_oaf_params.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/baseline_to_oaf_params.json @@ -3,5 +3,6 @@ {"paramName":"i", "paramLongName":"isLookupUrl", "paramDescription": "isLookupUrl", "paramRequired": true}, {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the path of the sequencial file to read", "paramRequired": true}, {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the oaf path ", "paramRequired": true}, + {"paramName":"s", "paramLongName":"skipUpdate", "paramDescription": "skip update ", "paramRequired": false}, {"paramName":"h", "paramLongName":"hdfsServerUri", "paramDescription": "the working path ", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/bio_to_oaf_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/bio_to_oaf_params.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/bio_to_oaf_params.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_download_update.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_download_update.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_download_update.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_to_df_params.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/ebi_to_df_params.json rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/ebi_to_df_params.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml new file mode 100644 index 000000000..4b47ae38e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/ebi/oozie_app/workflow.xml @@ -0,0 +1,105 @@ + + + + sourcePath + the Working Path + + + workingPath + the Working Path + + + targetPath + the OAF MDStore Path + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + resumeFrom + DownloadEBILinks + node to start + + + + + + + + ${wf:conf('resumeFrom') eq 'DownloadEBILinks'} + ${wf:conf('resumeFrom') eq 'CreateEBIDataSet'} + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + yarn-cluster + cluster + Incremental Download EBI Links + eu.dnetlib.dhp.sx.bio.ebi.SparkDownloadEBILinks + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=2000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --sourcePath${sourcePath} + --workingPath${workingPath} + --masteryarn + + + + + + + + + + + + + + + + yarn-cluster + cluster + Create OAF DataSet + eu.dnetlib.dhp.sx.bio.ebi.SparkEBILinksToOaf + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.sql.shuffle.partitions=2000 + ${sparkExtraOPT} + + --sourcePath${sourcePath}/ebi_links_dataset + --targetPath${targetPath} + --masteryarn + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/config-default.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml similarity index 71% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml rename to dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml index 914d1c2c7..8915a090b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/pubmed/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/sx/bio/pubmed/oozie_app/workflow.xml @@ -1,17 +1,22 @@ - + baselineWorkingPath the Baseline Working Path - - targetPath - the Target Path - isLookupUrl The IS lookUp service endopoint + + targetPath + The target path + + + skipUpdate + false + The request block size + @@ -24,9 +29,9 @@ yarn cluster - Convert Baseline to Dataset - eu.dnetlib.dhp.sx.graph.ebi.SparkCreateBaselineDataFrame - dhp-graph-mapper-${projectVersion}.jar + Convert Baseline to OAF Dataset + eu.dnetlib.dhp.sx.bio.ebi.SparkCreateBaselineDataFrame + dhp-aggregation-${projectVersion}.jar --executor-memory=${sparkExecutorMemory} --executor-cores=${sparkExecutorCores} @@ -41,6 +46,8 @@ --targetPath${targetPath} --masteryarn --isLookupUrl${isLookupUrl} + --hdfsServerUri${nameNode} + --skipUpdate${skipUpdate} diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/log4j.properties b/dhp-workflows/dhp-aggregation/src/main/resources/log4j.properties index 63cba917e..81458d1f7 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/log4j.properties +++ b/dhp-workflows/dhp-aggregation/src/main/resources/log4j.properties @@ -7,3 +7,6 @@ log4j.appender.A1=org.apache.log4j.ConsoleAppender # A1 uses PatternLayout. log4j.appender.A1.layout=org.apache.log4j.PatternLayout log4j.appender.A1.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n + +log4j.logger.org.apache.spark=FATAL +log4j.logger.org.spark_project=FATAL diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/datacite.md b/dhp-workflows/dhp-aggregation/src/site/markdown/datacite.md new file mode 100644 index 000000000..e69de29bb diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/index.md b/dhp-workflows/dhp-aggregation/src/site/markdown/index.md new file mode 100644 index 000000000..240617f91 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/index.md @@ -0,0 +1,20 @@ +##DHP-Aggregation + +This module defines a set of oozie workflows for + +1. the **collection** and **transformation** of metadata records. +2. the **integration** of new external information in the result + + +### Collection and Transformation + +The workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure +the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping +of each MDStore. + +It defines [mappings](mappings.md) for transformation of different datasource (See mapping section). + +### Integration of external information in the result + +The workflows create new entity in the OpenAIRE format (OAF) which aim is to enrich the result already contained in the graph. +See integration section for more insight diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md b/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md new file mode 100644 index 000000000..baf232e40 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/integration.md @@ -0,0 +1,36 @@ +DHP Aggregation - Integration method +===================================== + +The integration method can be applied every time new information, which is not aggregated from the repositories +nor computed directly by OpenAIRE, should be added to the results of the graph. + +The information integrated so far is: + +1. Article impact measures + 1. [Bip!Finder](https://dl.acm.org/doi/10.1145/3357384.3357850) scores +2. Result Subjects + 1. Integration of Fields od Science and Techonology ([FOS](https://www.qnrf.org/en-us/FOS)) classification in + results subjects. + + +The method always consists in the creation of a new entity in the OpenAIRE format (OAF entity) containing only the id +and the element in the OAF model that should be used to map the information we want to integrate. + +The id is set by using a particular encoding of the given PID + +*unresolved:[pid]:[pidtype]* + +where + +1. *unresolved* is a constant value +2. *pid* is the persistent id value, e.g. 10.5281/zenodo.4707307 +3. *pidtype* is the persistent id type, e.g. doi + +Such entities are matched against those available in the graph using the result.instance.pid values. + +This mechanism can be used to integrate enrichments produced as associated by a given PID. +If a match will be found with one of the results already in the graph that said result will be enriched with the information +present in the new OAF. +All the objects for which a match is not found are discarded. + + diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/introduction.md b/dhp-workflows/dhp-aggregation/src/site/markdown/introduction.md new file mode 100644 index 000000000..9da46a27e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/introduction.md @@ -0,0 +1,7 @@ +##DHP-Aggregation + +This module defines a set of oozie workflows for the **collection** and **transformation** of metadata records. + +Both workflows interact with the Metadata Store Manager (MdSM) to handle the logical transactions required to ensure +the consistency of the read/write operations on the data as the MdSM in fact keeps track of the logical-physical mapping +of each MDStore. \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/mappings.md b/dhp-workflows/dhp-aggregation/src/site/markdown/mappings.md new file mode 100644 index 000000000..576c4b6be --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/mappings.md @@ -0,0 +1,18 @@ +DHP Aggregation +=============== + +DHP-Aggregations contains different mappings from original data format into OAF Data Format, +which converge in the graph in different ways: + +- Via Action Manager +- Direct in the MdStore on Hadoop + +Below the list of the implemented mapping + + +Mappings +======= + +1. [PubMed](pubmed.md) +2. [Datacite](datacite.md) + diff --git a/dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md b/dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md new file mode 100644 index 000000000..c1813394b --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/site/markdown/pubmed.md @@ -0,0 +1,66 @@ +#Pubmed Mapping +This section describes the mapping implemented for [MEDLINE/PubMed](https://pubmed.ncbi.nlm.nih.gov/). + +Collection +--------- +The native data is collected from [ftp baseline](https://ftp.ncbi.nlm.nih.gov/pubmed/baseline/) containing XML with +the following [schema](https://www.nlm.nih.gov/bsd/licensee/elements_descriptions.html) + + +Parsing +------- +The resposible class of parsing is [PMParser](/dnet-hadoop/scaladocs/#eu.dnetlib.dhp.sx.bio.pubmed.PMParser) that generates +an intermediate mapping of PubMed Article defined [here](/dnet-hadoop/apidocs/eu/dnetlib/dhp/sx/bio/pubmed/package-summary.html) + + +Mapping +------- + +The table below describes the mapping from the XML Native to the OAF mapping + + + + + +| Xpath Source | Oaf Field | Notes | +| ----------- | ----------- | ----------- | +| //PMID | pid | classid = classname = pmid +| | **Instance Mapping** | | +|//PublicationType | InstanceType | If the article contains the typology **Journal Article** then we apply this type else We have to find a terms that match the vocabulary otherwise we discard it +|//PMID | instance/PID | Map the pmid also in the pid in the instance | +| //ArticleId[./@IdType="doi" | instance/alternateIdentifier |classid = classname = doi +|//PMID | instance/URL | prepend to the PMId the base url https://pubmed.ncbi.nlm.nih.gov/ +| //PubmedPubDate | instance/Dateofacceptance | apply the function GraphCleaningFunctions.cleanDate before assign it +| FOR ALL INSTANCE | CollectedFrom | datasourceName: *Europe PubMed Central* DatasourceId: +| | **Journal Mapping** | | +|//Journal/PubDate| Journal/Conferencedate | map the date of the Journal +|//Journal/Title| Journal/Name | | +|//Journal/Volume| Journal/Vol | | +|//Journal/ISSN| Journal/issPrinted | | +|//Journal/Issue| Journal/Iss | | +| | **Publication Mapping** | | +| //PubmedPubDate | Dateofacceptance | apply the function GraphCleaningFunctions.cleanDate before assign it +| //Title | title | with qualifier ModelConstants.MAIN_TITLE_QUALIFIER +| //AbstractText | Description || +|//Language| Language| cleaning vocabulary -> dnet:languages +|//DescriptorName| Subject | classId, className = keyword +| | **Author Mapping** | | +|//Author/LastName| author.Surname| | +|//Author/ForeName| author.Forename| | +|//Author/FullName| author.Forename| Concatenation of forname + lastName if exist | +|FOR ALL AUTHOR | author.rank| sequential number starting from 1| + +#TODO + +Missing item mapped + + + + + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/site/resources/images/openaire.png b/dhp-workflows/dhp-aggregation/src/site/resources/images/openaire.png new file mode 100644 index 000000000..00d320c39 Binary files /dev/null and b/dhp-workflows/dhp-aggregation/src/site/resources/images/openaire.png differ diff --git a/dhp-workflows/dhp-aggregation/src/site/site.xml b/dhp-workflows/dhp-aggregation/src/site/site.xml new file mode 100644 index 000000000..75fc5032e --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/site/site.xml @@ -0,0 +1,34 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java new file mode 100644 index 000000000..c48ccc8c2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/PrepareTest.java @@ -0,0 +1,250 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities; + +import static org.junit.jupiter.api.Assertions.*; + +import java.io.BufferedReader; +import java.io.IOException; +import java.io.InputStreamReader; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.stream.Collectors; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel; +import eu.dnetlib.dhp.common.collection.CollectorException; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class PrepareTest { + + private static final Logger log = LoggerFactory.getLogger(ProduceTest.class); + + private static Path workingDir; + private static SparkSession spark; + private static LocalFileSystem fs; + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(PrepareTest.class.getSimpleName()); + + fs = FileSystem.getLocal(new Configuration()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(ProduceTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(PrepareTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void bipPrepareTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json") + .getPath(); + + PrepareBipFinder + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + "--outputPath", workingDir.toString() + "/work" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/work/bip") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + + Assertions.assertEquals(86, tmp.count()); + + String doi1 = "unresolved::10.0000/096020199389707::doi"; + + Assertions.assertEquals(1, tmp.filter(r -> r.getId().equals(doi1)).count()); + Assertions.assertEquals(3, tmp.filter(r -> r.getId().equals(doi1)).collect().get(0).getMeasures().size()); + Assertions + .assertEquals( + "6.34596412687e-09", tmp + .filter(r -> r.getId().equals(doi1)) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(sl -> sl.getId().equals("influence")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "0.641151896994", tmp + .filter(r -> r.getId().equals(doi1)) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(sl -> sl.getId().equals("popularity_alt")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "2.33375102921e-09", tmp + .filter(r -> r.getId().equals(doi1)) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(sl -> sl.getId().equals("popularity")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + + } + + @Test + void getFOSFileTest() throws IOException, ClassNotFoundException { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/h2020_fos_sbs.csv") + .getPath(); + final String outputPath = workingDir.toString() + "/fos.json"; + + new GetFOSData() + .doRewrite( + sourcePath, outputPath, "eu.dnetlib.dhp.actionmanager.createunresolvedentities.model.FOSDataModel", + '\t', fs); + + BufferedReader in = new BufferedReader( + new InputStreamReader(fs.open(new org.apache.hadoop.fs.Path(outputPath)))); + + String line; + int count = 0; + while ((line = in.readLine()) != null) { + FOSDataModel fos = new ObjectMapper().readValue(line, FOSDataModel.class); + + System.out.println(new ObjectMapper().writeValueAsString(fos)); + count += 1; + } + + assertEquals(38, count); + + } + + @Test + void fosPrepareTest() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json") + .getPath(); + + PrepareFOSSparkJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", sourcePath, + + "-outputPath", workingDir.toString() + "/work" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/work/fos") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + + String doi1 = "unresolved::10.3390/s18072310::doi"; + + assertEquals(50, tmp.count()); + assertEquals(1, tmp.filter(row -> row.getId().equals(doi1)).count()); + assertTrue( + tmp + .filter(r -> r.getId().equals(doi1)) + .flatMap(r -> r.getSubject().iterator()) + .map(sbj -> sbj.getValue()) + .collect() + .contains("engineering and technology")); + + assertTrue( + tmp + .filter(r -> r.getId().equals(doi1)) + .flatMap(r -> r.getSubject().iterator()) + .map(sbj -> sbj.getValue()) + .collect() + .contains("nano-technology")); + assertTrue( + tmp + .filter(r -> r.getId().equals(doi1)) + .flatMap(r -> r.getSubject().iterator()) + .map(sbj -> sbj.getValue()) + .collect() + .contains("nanoscience & nanotechnology")); + + String doi = "unresolved::10.1111/1365-2656.12831::doi"; + assertEquals(1, tmp.filter(row -> row.getId().equals(doi)).count()); + assertTrue( + tmp + .filter(r -> r.getId().equals(doi)) + .flatMap(r -> r.getSubject().iterator()) + .map(sbj -> sbj.getValue()) + .collect() + .contains("psychology and cognitive sciences")); + + assertTrue( + tmp + .filter(r -> r.getId().equals(doi)) + .flatMap(r -> r.getSubject().iterator()) + .map(sbj -> sbj.getValue()) + .collect() + .contains("social sciences")); + assertFalse( + tmp + .filter(r -> r.getId().equals(doi)) + .flatMap(r -> r.getSubject().iterator()) + .map(sbj -> sbj.getValue()) + .collect() + .contains("NULL")); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java new file mode 100644 index 000000000..b77b5bb36 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/createunresolvedentities/ProduceTest.java @@ -0,0 +1,234 @@ + +package eu.dnetlib.dhp.actionmanager.createunresolvedentities; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.stream.Collectors; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; + +public class ProduceTest { + private static final Logger log = LoggerFactory.getLogger(ProduceTest.class); + + private static Path workingDir; + private static SparkSession spark; + private static LocalFileSystem fs; + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + private static final String ID_PREFIX = "50|doi_________"; + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(ProduceTest.class.getSimpleName()); + + fs = FileSystem.getLocal(new Configuration()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(ProduceTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(ProduceTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void produceTest() throws Exception { + + final String bipPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json") + .getPath(); + + PrepareBipFinder + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", bipPath, + "--outputPath", workingDir.toString() + "/work" + + }); + final String fosPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/createunresolvedentities/fos/fos.json") + .getPath(); + + PrepareFOSSparkJob + .main( + new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", fosPath, + "-outputPath", workingDir.toString() + "/work" + }); + + SparkSaveUnresolved.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--sourcePath", workingDir.toString() + "/work", + + "-outputPath", workingDir.toString() + "/unresolved" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/unresolved") + .map(item -> OBJECT_MAPPER.readValue(item, Result.class)); + + Assertions.assertEquals(135, tmp.count()); + + Assertions.assertEquals(1, tmp.filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi")).count()); + + Assertions + .assertEquals( + 3, tmp + .filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi")) + .collect() + .get(0) + .getSubject() + .size()); + + Assertions + .assertEquals( + 3, tmp + .filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi")) + .collect() + .get(0) + .getMeasures() + .size()); + + List sbjs = tmp + .filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi")) + .flatMap(row -> row.getSubject().iterator()) + .collect(); + + sbjs.forEach(sbj -> Assertions.assertEquals("FOS", sbj.getQualifier().getClassid())); + sbjs + .forEach( + sbj -> Assertions + .assertEquals( + "Fields of Science and Technology classification", sbj.getQualifier().getClassname())); + sbjs + .forEach( + sbj -> Assertions + .assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemeid())); + sbjs + .forEach( + sbj -> Assertions + .assertEquals(ModelConstants.DNET_SUBJECT_TYPOLOGIES, sbj.getQualifier().getSchemename())); + + sbjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getDeletedbyinference())); + sbjs.forEach(sbj -> Assertions.assertEquals(true, sbj.getDataInfo().getInferred())); + sbjs.forEach(sbj -> Assertions.assertEquals(false, sbj.getDataInfo().getInvisible())); + sbjs.forEach(sbj -> Assertions.assertEquals("", sbj.getDataInfo().getTrust())); + sbjs.forEach(sbj -> Assertions.assertEquals("update", sbj.getDataInfo().getInferenceprovenance())); + sbjs + .forEach( + sbj -> Assertions.assertEquals("subject:fos", sbj.getDataInfo().getProvenanceaction().getClassid())); + sbjs + .forEach( + sbj -> Assertions + .assertEquals("Inferred by OpenAIRE", sbj.getDataInfo().getProvenanceaction().getClassname())); + sbjs + .forEach( + sbj -> Assertions + .assertEquals( + ModelConstants.DNET_PROVENANCE_ACTIONS, sbj.getDataInfo().getProvenanceaction().getSchemeid())); + sbjs + .forEach( + sbj -> Assertions + .assertEquals( + ModelConstants.DNET_PROVENANCE_ACTIONS, + sbj.getDataInfo().getProvenanceaction().getSchemename())); + + sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("engineering and technology")); + sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("nano-technology")); + sbjs.stream().anyMatch(sbj -> sbj.getValue().equals("nanoscience & nanotechnology")); + + List measures = tmp + .filter(row -> row.getId().equals("unresolved::10.3390/s18072310::doi")) + .flatMap(row -> row.getMeasures().iterator()) + .collect(); + Assertions + .assertEquals( + "7.5597134689e-09", measures + .stream() + .filter(mes -> mes.getId().equals("influence")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + + Assertions + .assertEquals( + "4.903880192", measures + .stream() + .filter(mes -> mes.getId().equals("popularity_alt")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + + Assertions + .assertEquals( + "1.17977512835e-08", measures + .stream() + .filter(mes -> mes.getId().equals("popularity")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + + Assertions + .assertEquals( + 49, tmp + .filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi")) + .filter(row -> row.getSubject() != null) + .count()); + + Assertions + .assertEquals( + 85, + tmp + .filter(row -> !row.getId().equals("unresolved::10.3390/s18072310::doi")) + .filter(r -> r.getMeasures() != null) + .count()); + + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala deleted file mode 100644 index a795a910d..000000000 --- a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/datacite/DataciteToOAFTest.scala +++ /dev/null @@ -1,57 +0,0 @@ -package eu.dnetlib.dhp.actionmanager.datacite - - -import com.fasterxml.jackson.databind.ObjectMapper -import com.fasterxml.jackson.databind.SerializationFeature -import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest -import eu.dnetlib.dhp.schema.oaf.Oaf -import org.junit.jupiter.api.extension.ExtendWith -import org.junit.jupiter.api.{BeforeEach, Test} -import org.mockito.junit.jupiter.MockitoExtension - -import java.text.SimpleDateFormat -import java.util.Locale -import scala.io.Source - -@ExtendWith(Array(classOf[MockitoExtension])) -class DataciteToOAFTest extends AbstractVocabularyTest{ - - - @BeforeEach - def setUp() :Unit = { - - super.setUpVocabulary() - } - - - @Test - def testDateMapping:Unit = { - val inputDate = "2021-07-14T11:52:54+0000" - val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US) - val dt = ISO8601FORMAT.parse(inputDate) - println(dt.getTime) - - - } - - - @Test - def testMapping() :Unit = { - val record =Source.fromInputStream(getClass.getResourceAsStream("record.json")).mkString - - - - val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT) - val res:List[Oaf] =DataciteToOAFTransformation.generateOAF(record, 0L,0L, vocabularies, true ) - - res.foreach(r => { - println (mapper.writeValueAsString(r)) - println("----------------------------") - - }) - - - - } - -} \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java new file mode 100644 index 000000000..5a04dcefe --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/opencitations/CreateOpenCitationsASTest.java @@ -0,0 +1,335 @@ + +package eu.dnetlib.dhp.actionmanager.opencitations; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Relation; +import eu.dnetlib.dhp.schema.oaf.utils.CleaningFunctions; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; + +public class CreateOpenCitationsASTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(CreateOpenCitationsASTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(CreateOpenCitationsASTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(CreateOpenCitationsASTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(CreateOpenCitationsASTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testNumberofRelations() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-shouldDuplicateRels", + Boolean.TRUE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + assertEquals(60, tmp.count()); + + // tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + + } + + @Test + void testNumberofRelations2() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + assertEquals(44, tmp.count()); + + // tmp.foreach(r -> System.out.println(OBJECT_MAPPER.writeValueAsString(r))); + + } + + @Test + void testRelationsCollectedFrom() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals(ModelConstants.OPENOCITATIONS_NAME, r.getCollectedfrom().get(0).getValue()); + assertEquals(ModelConstants.OPENOCITATIONS_ID, r.getCollectedfrom().get(0).getKey()); + }); + + } + + @Test + void testRelationsDataInfo() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals(false, r.getDataInfo().getInferred()); + assertEquals(false, r.getDataInfo().getDeletedbyinference()); + assertEquals("0.91", r.getDataInfo().getTrust()); + assertEquals( + CreateActionSetSparkJob.OPENCITATIONS_CLASSID, r.getDataInfo().getProvenanceaction().getClassid()); + assertEquals( + CreateActionSetSparkJob.OPENCITATIONS_CLASSNAME, r.getDataInfo().getProvenanceaction().getClassname()); + assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemeid()); + assertEquals(ModelConstants.DNET_PROVENANCE_ACTIONS, r.getDataInfo().getProvenanceaction().getSchemename()); + }); + + } + + @Test + void testRelationsSemantics() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals("citation", r.getSubRelType()); + assertEquals("resultResult", r.getRelType()); + }); + assertEquals(22, tmp.filter(r -> r.getRelClass().equals("Cites")).count()); + assertEquals(22, tmp.filter(r -> r.getRelClass().equals("IsCitedBy")).count()); + + } + + @Test + void testRelationsSourceTargetPrefix() throws Exception { + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + tmp.foreach(r -> { + assertEquals("50|doi_________::", r.getSource().substring(0, 17)); + assertEquals("50|doi_________::", r.getTarget().substring(0, 17)); + }); + + } + + @Test + void testRelationsSourceTargetCouple() throws Exception { + final String doi1 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-015-3684-x")); + final String doi2 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1111/j.1551-2916.2008.02408.x")); + final String doi3 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-014-2114-9")); + final String doi4 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/j.ceramint.2013.09.069")); + final String doi5 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1007/s10854-009-9913-4")); + final String doi6 = "50|doi_________::" + + IdentifierFactory.md5(CleaningFunctions.normalizePidValue("doi", "10.1016/0038-1098(72)90370-5")); + + String inputPath = getClass() + .getResource( + "/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles") + .getPath(); + + CreateActionSetSparkJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputPath", + inputPath, + "-outputPath", + workingDir.toString() + "/actionSet" + }); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(value -> OBJECT_MAPPER.readValue(value._2().toString(), AtomicAction.class)) + .map(aa -> ((Relation) aa.getPayload())); + + JavaRDD check = tmp.filter(r -> r.getSource().equals(doi1) || r.getTarget().equals(doi1)); + + assertEquals(10, check.count()); + + check.foreach(r -> { + if (r.getSource().equals(doi2) || r.getSource().equals(doi3) || r.getSource().equals(doi4) || + r.getSource().equals(doi5) || r.getSource().equals(doi6)) { + assertEquals(ModelConstants.IS_CITED_BY, r.getRelClass()); + assertEquals(doi1, r.getTarget()); + } + }); + + assertEquals(5, check.filter(r -> r.getSource().equals(doi1)).count()); + check.filter(r -> r.getSource().equals(doi1)).foreach(r -> assertEquals(ModelConstants.CITES, r.getRelClass())); + + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala new file mode 100644 index 000000000..477a4326a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -0,0 +1,113 @@ +package eu.dnetlib.dhp.datacite + + +import com.fasterxml.jackson.databind.{ObjectMapper, SerializationFeature} +import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest +import eu.dnetlib.dhp.schema.oaf.Oaf +import org.apache.commons.io.FileUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.functions.{col, count} +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.junit.jupiter.api.extension.ExtendWith +import org.junit.jupiter.api.{AfterEach, BeforeEach, Test} +import org.mockito.junit.jupiter.MockitoExtension +import org.slf4j.{Logger, LoggerFactory} + +import java.nio.file.{Files, Path} +import java.text.SimpleDateFormat +import java.util.Locale +import scala.io.Source +import org.junit.jupiter.api.Assertions._ +@ExtendWith(Array(classOf[MockitoExtension])) +class DataciteToOAFTest extends AbstractVocabularyTest{ + + private var workingDir:Path = null + val log: Logger = LoggerFactory.getLogger(getClass) + + @BeforeEach + def setUp() :Unit = { + + workingDir= Files.createTempDirectory(getClass.getSimpleName) + super.setUpVocabulary() + } + + @AfterEach + def tearDown() :Unit = { + FileUtils.deleteDirectory(workingDir.toFile) + } + + + @Test + def testDateMapping:Unit = { + val inputDate = "2021-07-14T11:52:54+0000" + val ISO8601FORMAT = new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ssZ", Locale.US) + val dt = ISO8601FORMAT.parse(inputDate) + println(dt.getTime) + + + } + + + @Test + def testConvert(): Unit = { + + + val path = getClass.getResource("/eu/dnetlib/dhp/actionmanager/datacite/dataset").getPath + + val conf = new SparkConf() + val spark:SparkSession = SparkSession.builder().config(conf) + .appName(getClass.getSimpleName) + .master("local[*]") + .getOrCreate() + + + + implicit val oafEncoder:Encoder[Oaf] = Encoders.kryo[Oaf] + val instance = new GenerateDataciteDatasetSpark(null, null, log) + val targetPath = s"$workingDir/result" + + instance.generateDataciteDataset(path, exportLinks = true, vocabularies,targetPath, spark) + + import spark.implicits._ + + val nativeSize =spark.read.load(path).count() + + + assertEquals(100, nativeSize) + + val result:Dataset[Oaf] = spark.read.load(targetPath).as[Oaf] + + + result.map(s => s.getClass.getSimpleName).groupBy(col("value").alias("class")).agg(count("value").alias("Total")).show(false) + + val t = spark.read.load(targetPath).count() + + assertTrue(t >0) + + + spark.stop() + + + + + } + + + @Test + def testMapping() :Unit = { + val record =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/record.json")).mkString + + val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT) + val res:List[Oaf] =DataciteToOAFTransformation.generateOAF(record, 0L,0L, vocabularies, true ) + + res.foreach(r => { + println (mapper.writeValueAsString(r)) + println("----------------------------") + + }) + + + + } + +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala similarity index 92% rename from dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala rename to dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala index 87279eb21..893a6e628 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/BioScholixTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/sx/bio/BioScholixTest.scala @@ -1,13 +1,10 @@ -package eu.dnetlib.dhp.sx.graph.bio.pubmed +package eu.dnetlib.dhp.sx.bio import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} -import eu.dnetlib.dhp.schema.common.ModelConstants -import eu.dnetlib.dhp.schema.oaf.utils.{CleaningFunctions, OafMapperUtils, PidType} +import eu.dnetlib.dhp.aggregation.AbstractVocabularyTest import eu.dnetlib.dhp.schema.oaf.{Oaf, Relation, Result} -import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF.ScholixResolved -import eu.dnetlib.dhp.sx.graph.bio.BioDBToOAF -import eu.dnetlib.dhp.sx.graph.bio.pubmed.PubMedToOaf.dataInfo -import eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks +import eu.dnetlib.dhp.sx.bio.BioDBToOAF.ScholixResolved +import eu.dnetlib.dhp.sx.bio.pubmed.{PMArticle, PMParser, PubMedToOaf} import org.json4s.DefaultFormats import org.json4s.JsonAST.{JField, JObject, JString} import org.json4s.jackson.JsonMethods.parse @@ -55,7 +52,7 @@ class BioScholixTest extends AbstractVocabularyTest{ @Test def testEBIData() = { - val inputXML = Source.fromInputStream(getClass.getResourceAsStream("pubmed.xml")).mkString + val inputXML = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml")).mkString val xml = new XMLEventReader(Source.fromBytes(inputXML.getBytes())) new PMParser(xml).foreach(s =>println(mapper.writeValueAsString(s))) } @@ -65,7 +62,7 @@ class BioScholixTest extends AbstractVocabularyTest{ def testPubmedToOaf(): Unit = { assertNotNull(vocabularies) assertTrue(vocabularies.vocabularyExists("dnet:publication_resource")) - val records:String =Source.fromInputStream(getClass.getResourceAsStream("pubmed_dump")).mkString + val records:String =Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump")).mkString val r:List[Oaf] = records.lines.toList.map(s=>mapper.readValue(s, classOf[PMArticle])).map(a => PubMedToOaf.convert(a, vocabularies)) assertEquals(10, r.size) assertTrue(r.map(p => p.asInstanceOf[Result]).flatMap(p => p.getInstance().asScala.map(i => i.getInstancetype.getClassid)).exists(p => "0037".equalsIgnoreCase(p))) diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json new file mode 100644 index 000000000..03cef4be1 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/createunresolvedentities/bip/bip.json @@ -0,0 +1,86 @@ +{"10.3390/s18072310": [{"id": "influence", "unit": [{"value": "7.5597134689e-09", "key": "score"}]}, {"id": 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+02001000007362801000805046300010563030608056309-02001000106361937281010370200010437000937000308,10.1007/s10854-015-3685-9,10.1016/j.saa.2014.09.038,2015-09-03,P0Y7M,no,no +02001000007362801000805046300010563030608056309-0200100010636193722102912171027370200010537000437000106,10.1007/s10854-015-3685-9,10.1016/j.matchar.2015.04.016,2015-09-03,P0Y2M,no,no \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input2 b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input2 new file mode 100644 index 000000000..14ee8b354 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input2 @@ -0,0 +1,8 @@ +oci,citing,cited,creation,timespan,journal_sc,author_sc +02001000308362804010509076300010963000003086301-0200100020936020001003227000009010004,10.1038/s41597-019-0038-1,10.1029/2010wr009104,2019-04-15,P8Y1M,no,no +02001000308362804010509076300010963000003086301-0200100010636280103060463080105025800015900000006006303,10.1038/s41597-019-0038-1,10.1016/s1364-8152(01)00060-3,2019-04-15,P17Y3M,no,no +02001000308362804010509076300010963000003086301-02001000007362800000407076300010063000401066333,10.1038/s41597-019-0038-1,10.1007/s00477-010-0416-x,2019-04-15,P8Y9M6D,no,no +02001000308362804010509076300010963000003086301-02001000007362800000700046300010363000905016308,10.1038/s41597-019-0038-1,10.1007/s00704-013-0951-8,2019-04-15,P5Y9M23D,no,no +02001000308362804010509076300010963000003086301-02001000002361924123705070707,10.1038/s41597-019-0038-1,10.1002/joc.5777,2019-04-15,P0Y8M1D,no,no +02001000308362804010509076300010963000003086301-02005010904361714282863020263040504076302000108,10.1038/s41597-019-0038-1,10.5194/hess-22-4547-2018,2019-04-15,P0Y7M18D,no,no +02001000308362804010509076300010963000003086301-02001000002361924123703050404,10.1038/s41597-019-0038-1,10.1002/joc.3544,2019-04-15,P6Y9M6D,no,no \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input3 b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input3 new file mode 100644 index 000000000..0611929d5 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/actionmanager/opencitations/inputFiles/input3 @@ -0,0 +1,9 @@ +oci,citing,cited,creation,timespan,journal_sc,author_sc +0200100000236090708010101090307000202023727141528-020050302063600040000010307,10.1002/9781119370222.refs,10.5326/0400137,2020-06-22,P16Y3M,no,no +0200100000236090708010101090307000202023727141528-0200101010136193701050302630905003337020000073700000301093733,10.1002/9781119370222.refs,10.1111/j.1532-950x.2007.00319.x,2020-06-22,P12Y8M,no,no +0200100000236090708010101090307000202023727141528-0200101010136312830370102030509,10.1002/9781119370222.refs,10.1111/vsu.12359,2020-06-22,P4Y10M29D,no,no +0200100000236090708010101090307000202023727141528-020050302063600030900020904,10.1002/9781119370222.refs,10.5326/0390294,2020-06-22,P17Y1M,no,no +0200100000236090708010101090307000202023727141528-020050302063600040200030701,10.1002/9781119370222.refs,10.5326/0420371,2020-06-22,P13Y9M,no,no +0200100000236090708010101090307000202023727141528-0200101010136193701050302630905003337020001033701020000003733,10.1002/9781119370222.refs,10.1111/j.1532-950x.2013.12000.x,2020-06-22,P7Y2M,no,no +0200100000236090708010101090307000202023727141528-020010008003600000408000106093702000006370306070200,10.1002/9781119370222.refs,10.1080/00480169.2006.36720,2020-06-22,P13Y6M,no,no +0200100000236090708010101090307000202023727141528-0200101010136193701070501630008010337020000063700000003033733,10.1002/9781119370222.refs,10.1111/j.1751-0813.2006.00033.x,2020-06-22,P13Y8M,no,no \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/crossref_links b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/crossref_links similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/crossref_links rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/crossref_links diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ebi_links.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ebi_links.gz similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ebi_links.gz rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ebi_links.gz diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ls_result similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/ls_result rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/ls_result diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pdb_dump b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pdb_dump similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pdb_dump rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pdb_dump diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed.xml rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed_dump b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed_dump rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed_dump diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/scholix_resolved diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump rename to dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/uniprot_dump diff --git a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java index 38ffd28fe..7d0d6b0b8 100644 --- a/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java +++ b/dhp-workflows/dhp-blacklist/src/main/java/eu/dnetlib/dhp/blacklist/ReadBlacklistFromDB.java @@ -91,8 +91,8 @@ public class ReadBlacklistFromDB implements Closeable { String encoding = rs.getString("relationship"); RelationInverse ri = ModelSupport.relationInverseMap.get(encoding); - direct.setRelClass(ri.getRelation()); - inverse.setRelClass(ri.getInverse()); + direct.setRelClass(ri.getRelClass()); + inverse.setRelClass(ri.getInverseRelClass()); direct.setRelType(ri.getRelType()); inverse.setRelType(ri.getRelType()); direct.setSubRelType(ri.getSubReltype()); diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java index 45bfc785f..52e9917bb 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/UpdateMatcherTest.java @@ -19,7 +19,7 @@ import eu.dnetlib.dhp.broker.oa.matchers.simple.EnrichMissingPublicationDate; import eu.dnetlib.dhp.broker.oa.util.UpdateInfo; @ExtendWith(MockitoExtension.class) -class UpdateMatcherTest { +public class UpdateMatcherTest { UpdateMatcher matcher = new EnrichMissingPublicationDate(); diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java index 550ded9f4..5af81a31a 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/matchers/simple/EnrichMissingPublicationDateTest.java @@ -11,7 +11,7 @@ import org.junit.jupiter.api.Test; import eu.dnetlib.broker.objects.OaBrokerMainEntity; -class EnrichMissingPublicationDateTest { +public class EnrichMissingPublicationDateTest { final EnrichMissingPublicationDate matcher = new EnrichMissingPublicationDate(); diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java index b532aa9f7..d93390e4a 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/SubscriptionUtilsTest.java @@ -8,7 +8,7 @@ import java.util.Arrays; import org.junit.jupiter.api.Test; -class SubscriptionUtilsTest { +public class SubscriptionUtilsTest { @Test void testVerifyListSimilar() { diff --git a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java index a8bc03e31..117bdeef4 100644 --- a/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java +++ b/dhp-workflows/dhp-broker-events/src/test/java/eu/dnetlib/dhp/broker/oa/util/TrustUtilsTest.java @@ -9,7 +9,7 @@ import eu.dnetlib.broker.objects.OaBrokerAuthor; import eu.dnetlib.broker.objects.OaBrokerMainEntity; import eu.dnetlib.broker.objects.OaBrokerTypedValue; -class TrustUtilsTest { +public class TrustUtilsTest { private static final double THRESHOLD = 0.95; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java index 6a9b21b00..136413376 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/AbstractSparkAction.java @@ -139,14 +139,28 @@ abstract class AbstractSparkAction implements Serializable { protected boolean isOpenorgs(Relation rel) { return Optional .ofNullable(rel.getCollectedfrom()) - .map( - c -> c - .stream() - .filter(Objects::nonNull) - .anyMatch(kv -> ModelConstants.OPENORGS_NAME.equals(kv.getValue()))) + .map(c -> isCollectedFromOpenOrgs(c)) .orElse(false); } + protected boolean isOpenorgsDedupRel(Relation rel) { + return isOpenorgs(rel) && isOpenOrgsDedupMergeRelation(rel); + } + + private boolean isCollectedFromOpenOrgs(List c) { + return c + .stream() + .filter(Objects::nonNull) + .anyMatch(kv -> ModelConstants.OPENORGS_NAME.equals(kv.getValue())); + } + + private boolean isOpenOrgsDedupMergeRelation(Relation rel) { + return ModelConstants.ORG_ORG_RELTYPE.equals(rel.getRelType()) && + ModelConstants.DEDUP.equals(rel.getSubRelType()) + && (ModelConstants.IS_MERGED_IN.equals(rel.getRelClass()) || + ModelConstants.MERGES.equals(rel.getRelClass())); + } + protected static Boolean parseECField(Field field) { if (field == null) return null; diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java index d79d24653..aeb485768 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/DedupUtility.java @@ -14,6 +14,9 @@ import org.xml.sax.SAXException; import com.google.common.collect.Sets; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -152,4 +155,25 @@ public class DedupUtility { return o1.compareTo(o2); } + public static Relation createSimRel(String source, String target, String entity) { + final Relation r = new Relation(); + r.setSource(source); + r.setTarget(target); + r.setSubRelType("dedupSimilarity"); + r.setRelClass(ModelConstants.IS_SIMILAR_TO); + r.setDataInfo(new DataInfo()); + + switch (entity) { + case "result": + r.setRelType(ModelConstants.RESULT_RESULT); + break; + case "organization": + r.setRelType(ModelConstants.ORG_ORG_RELTYPE); + break; + default: + throw new IllegalArgumentException("unmanaged entity type: " + entity); + } + return r; + } + } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCopyRelationsNoOpenorgs.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCopyRelationsNoOpenorgs.java index bf0b7f687..62cbb5bff 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCopyRelationsNoOpenorgs.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCopyRelationsNoOpenorgs.java @@ -61,9 +61,11 @@ public class SparkCopyRelationsNoOpenorgs extends AbstractSparkAction { .textFile(relationPath) .map(patchRelFn(), Encoders.bean(Relation.class)) .toJavaRDD() - .filter(x -> !isOpenorgs(x)); + .filter(x -> !isOpenorgsDedupRel(x)); - log.info("Number of non-Openorgs relations collected: {}", simRels.count()); + if (log.isDebugEnabled()) { + log.debug("Number of non-Openorgs relations collected: {}", simRels.count()); + } spark .createDataset(simRels.rdd(), Encoders.bean(Relation.class)) diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java index f89f634b5..3aa8f241d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkCreateSimRels.java @@ -20,6 +20,7 @@ import org.xml.sax.SAXException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.dedup.model.Block; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.utils.ISLookupClientFactory; @@ -102,7 +103,7 @@ public class SparkCreateSimRels extends AbstractSparkAction { .createDataset( Deduper .computeRelations(sc, blocks, dedupConf) - .map(t -> createSimRel(t._1(), t._2(), entity)) + .map(t -> DedupUtility.createSimRel(t._1(), t._2(), entity)) .repartition(numPartitions) .rdd(), Encoders.bean(Relation.class)); @@ -111,24 +112,4 @@ public class SparkCreateSimRels extends AbstractSparkAction { } } - private Relation createSimRel(String source, String target, String entity) { - final Relation r = new Relation(); - r.setSource(source); - r.setTarget(target); - r.setSubRelType("dedupSimilarity"); - r.setRelClass("isSimilarTo"); - r.setDataInfo(new DataInfo()); - - switch (entity) { - case "result": - r.setRelType("resultResult"); - break; - case "organization": - r.setRelType("organizationOrganization"); - break; - default: - throw new IllegalArgumentException("unmanaged entity type: " + entity); - } - return r; - } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java index 7d91e47cc..1cfac9a27 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/SparkWhitelistSimRels.java @@ -124,31 +124,12 @@ public class SparkWhitelistSimRels extends AbstractSparkAction { Dataset whiteListSimRels = whiteListRels2 .map( - (MapFunction, Relation>) r -> createSimRel(r._1(), r._2(), entity), + (MapFunction, Relation>) r -> DedupUtility + .createSimRel(r._1(), r._2(), entity), Encoders.bean(Relation.class)); saveParquet(whiteListSimRels, outputPath, SaveMode.Append); } } - private Relation createSimRel(String source, String target, String entity) { - final Relation r = new Relation(); - r.setSource(source); - r.setTarget(target); - r.setSubRelType("dedupSimilarity"); - r.setRelClass("isSimilarTo"); - r.setDataInfo(new DataInfo()); - - switch (entity) { - case "result": - r.setRelType("resultResult"); - break; - case "organization": - r.setRelType("organizationOrganization"); - break; - default: - throw new IllegalArgumentException("unmanaged entity type: " + entity); - } - return r; - } } diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml index 83a47ea6c..4ea003926 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-dedup-openaire/src/main/resources/eu/dnetlib/dhp/oa/dedup/consistency/oozie_app/workflow.xml @@ -89,7 +89,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=15000 --graphBasePath${graphBasePath} --o${graphOutputPath} @@ -114,7 +114,7 @@ --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - --conf spark.sql.shuffle.partitions=7680 + --conf spark.sql.shuffle.partitions=15000 --graphInputPath${graphBasePath} --outputPath${workingPath}/grouped_entities diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsProvisionTest.java b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsProvisionTest.java index 2349ffebe..2a9f34dee 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsProvisionTest.java +++ b/dhp-workflows/dhp-dedup-openaire/src/test/java/eu/dnetlib/dhp/oa/dedup/SparkOpenorgsProvisionTest.java @@ -11,6 +11,8 @@ import java.io.IOException; import java.io.Serializable; import java.net.URISyntaxException; import java.nio.file.Paths; +import java.util.List; +import java.util.stream.Collectors; import org.apache.commons.io.FileUtils; import org.apache.commons.io.IOUtils; @@ -29,6 +31,8 @@ import org.mockito.Mock; import org.mockito.Mockito; import org.mockito.junit.jupiter.MockitoExtension; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; @@ -226,9 +230,10 @@ public class SparkOpenorgsProvisionTest implements Serializable { new SparkCopyRelationsNoOpenorgs(parser, spark).run(isLookUpService); - long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); + final JavaRDD rels = jsc.textFile(testDedupGraphBasePath + "/relation"); + + assertEquals(2382, rels.count()); - assertEquals(2380, relations); } @Test @@ -250,7 +255,7 @@ public class SparkOpenorgsProvisionTest implements Serializable { long relations = jsc.textFile(testDedupGraphBasePath + "/relation").count(); - assertEquals(4894, relations); + assertEquals(4896, relations); // check deletedbyinference final Dataset mergeRels = spark diff --git a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/openorgs/provision/relation/part-00000 b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/openorgs/provision/relation/part-00000 index 67d491ca2..35d92089d 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/openorgs/provision/relation/part-00000 +++ b/dhp-workflows/dhp-dedup-openaire/src/test/resources/eu/dnetlib/dhp/dedup/openorgs/provision/relation/part-00000 @@ -2518,3 +2518,5 @@ {"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::5c351d85f02db01ca291acd119f0bd78", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|opendoar____::37248e2f6987b18670dd2b8a51d6ef55", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []} {"subRelType": "dedup", "relClass": "merges", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []} {"subRelType": "dedup", "relClass": "isMergedIn", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []} +{"subRelType": "relationship", "relClass": "IsParentOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []} +{"subRelType": "relationship", "relClass": "IsChildOf", "dataInfo": {"provenanceaction": {"classid": "sysimport:crosswalk:entityregistry", "classname": "sysimport:crosswalk:entityregistry", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": false, "inferenceprovenance": "", "invisible": false, "trust": "0.990"}, "target": "20|corda_______::6acb33e6ea8c6fcdabc891c80d083c64", "lastupdatetimestamp": 1617801137807, "relType": "organizationOrganization", "source": "20|openorgs____::e38c1a27fcb0f0ab218828e4f5fc7be9", "validationDate": null, "collectedfrom": [{"dataInfo": null, "key": "10|openaire____::0362fcdb3076765d9c0041ad331553e8", "value": "OpenOrgs Database"}], "validated": false, "properties": []} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index c08e09f53..501073e74 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -206,7 +206,7 @@ object SparkGenerateDoiBoost { (r.getSource, r) else if (r.getTarget.startsWith("unresolved")) (r.getTarget,r) - else + else ("resolved", r) })(Encoders.tuple(Encoders.STRING, mapEncoderRel)) @@ -221,7 +221,7 @@ object SparkGenerateDoiBoost { currentRels.setSource(currentOrgs._1) else currentRels.setTarget(currentOrgs._1) - currentRels + currentRels }.filter(r=> !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostPublicationAffiliation") magPubs.joinWith(a,magPubs("_1").equalTo(a("PaperId"))).map( item => { @@ -242,6 +242,6 @@ object SparkGenerateDoiBoost { else null }).filter(o=> o!=null).write.mode(SaveMode.Overwrite).save(s"$workingDirPath/doiBoostOrganization") - } + } -} \ No newline at end of file +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index 0ce55a96b..1262dd307 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -70,7 +70,7 @@ case object Crossref2Oaf { "reference-book" -> "0002 Book", "monograph" -> "0002 Book", "journal-article" -> "0001 Article", - "dissertation" -> "0006 Doctoral thesis", + "dissertation" -> "0044 Thesis", "other" -> "0038 Other literature type", "peer-review" -> "0015 Review", "proceedings" -> "0004 Conference object", @@ -206,11 +206,16 @@ case object Crossref2Oaf { else { instance.setDateofacceptance(asField(createdDate.getValue)) } - val s: String = (json \ "URL").extract[String] - val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null).distinct - if (links.nonEmpty) { - instance.setUrl(links.asJava) - } + val s: List[String] = List("https://doi.org/" + doi) +// val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct +// if (links.nonEmpty) { +// instance.setUrl(links.asJava) +// } + if(s.nonEmpty) + { + instance.setUrl(s.asJava) + } + result.setInstance(List(instance).asJava) //IMPORTANT diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala index ecb389af8..0ea4b66a4 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/mag/SparkProcessMAG.scala @@ -111,26 +111,9 @@ object SparkProcessMAG { .map(item => ConversionUtil.updatePubsWithConferenceInfo(item)) .write .mode(SaveMode.Overwrite) - .save(s"$workingPath/merge_step_2_conference") - - - magPubs= spark.read.load(s"$workingPath/merge_step_2_conference").as[Publication] - .map(p => (ConversionUtil.extractMagIdentifier(p.getOriginalId.asScala), p)).as[(String, Publication)] - - val paperUrlDataset = spark.read.load(s"$sourcePath/PaperUrls").as[MagPaperUrl].groupBy("PaperId").agg(collect_list(struct("sourceUrl")).as("instances")).as[MagUrl] - - - logger.info("Phase 5) enrich publication with URL and Instances") - magPubs.joinWith(paperUrlDataset, col("_1").equalTo(paperUrlDataset("PaperId")), "left") - .map { a: ((String, Publication), MagUrl) => ConversionUtil.addInstances((a._1._2, a._2)) } - .write.mode(SaveMode.Overwrite) .save(s"$workingPath/merge_step_3") -// logger.info("Phase 6) Enrich Publication with description") -// val pa = spark.read.load(s"${parser.get("sourcePath")}/PaperAbstractsInvertedIndex").as[MagPaperAbstract] -// pa.map(ConversionUtil.transformPaperAbstract).write.mode(SaveMode.Overwrite).save(s"${parser.get("targetPath")}/PaperAbstract") - val paperAbstract = spark.read.load((s"$workingPath/PaperAbstract")).as[MagPaperAbstract] @@ -162,12 +145,14 @@ object SparkProcessMAG { .write.mode(SaveMode.Overwrite) .save(s"$workingPath/mag_publication") + spark.read.load(s"$workingPath/mag_publication").as[Publication] + .filter(p => p.getId != null) + .groupByKey(p => p.getId) + .reduceGroups((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b)) + .map(_._2) + .write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication") - val s:RDD[Publication] = spark.read.load(s"$workingPath/mag_publication").as[Publication] - .map(p=>Tuple2(p.getId, p)).rdd.reduceByKey((a:Publication, b:Publication) => ConversionUtil.mergePublication(a,b)) - .map(_._2) - spark.createDataset(s).as[Publication].write.mode(SaveMode.Overwrite).save(s"$targetPath/magPublication") } } diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml index ab3b9593e..40a17b486 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/preprocess/oozie_app/workflow.xml @@ -107,7 +107,6 @@ - diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala index 75fb3f787..5ef92cfa4 100644 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/crossref/CrossrefMappingTest.scala @@ -612,4 +612,26 @@ class CrossrefMappingTest { } + @Test + def testMultipleURLs() :Unit = { + val json = Source.fromInputStream(getClass.getResourceAsStream("multiple_urls.json")).mkString + + + assertNotNull(json) + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + + val item : Result = resultList.filter(p => p.isInstanceOf[Result]).head.asInstanceOf[Result] + + assertEquals(1, item.getInstance().size()) + assertEquals(1, item.getInstance().get(0).getUrl().size()) + assertEquals("https://doi.org/10.1016/j.jas.2019.105013", item.getInstance().get(0).getUrl().get(0)) + //println(mapper.writeValueAsString(item)) + + } + } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/multiple_urls.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/multiple_urls.json new file mode 100644 index 000000000..5f90feac4 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/multiple_urls.json @@ -0,0 +1,614 @@ + +{ +"indexed": { +"date-parts": [ +[ +2021, +10, +31 +] +], +"date-time": "2021-10-31T15:48:01Z", +"timestamp": 1635695281393 +}, +"reference-count": 39, +"publisher": "Elsevier BV", +"license": [ +{ +"start": { +"date-parts": [ +[ +2019, +12, +1 +] +], +"date-time": "2019-12-01T00:00:00Z", +"timestamp": 1575158400000 +}, +"content-version": "tdm", +"delay-in-days": 0, +"URL": "https://www.elsevier.com/tdm/userlicense/1.0/" +}, +{ +"start": { +"date-parts": [ +[ +2019, +9, +13 +] +], +"date-time": "2019-09-13T00:00:00Z", +"timestamp": 1568332800000 +}, +"content-version": "vor", +"delay-in-days": 0, +"URL": "http://creativecommons.org/licenses/by/4.0/" +} +], +"funder": [ +{ +"DOI": "10.13039/100001182", +"name": "INSTAP", +"doi-asserted-by": "publisher" +}, +{ +"DOI": "10.13039/100014440", +"name": "Ministry of Science, Innovation and Universities", +"doi-asserted-by": "publisher", +"award": [ +"RYC-2016-19637" +] +}, +{ +"DOI": "10.13039/100010661", +"name": "European Union’s Horizon 2020", +"doi-asserted-by": "publisher", +"award": [ +"746446" +] +} +], +"content-domain": { +"domain": [ +"elsevier.com", +"sciencedirect.com" +], +"crossmark-restriction": true +}, +"short-container-title": [ +"Journal of Archaeological Science" +], +"published-print": { +"date-parts": [ +[ +2019, +12 +] +] +}, +"DOI": "10.1016/j.jas.2019.105013", +"type": "journal-article", +"created": { +"date-parts": [ +[ +2019, +9, +25 +] +], +"date-time": "2019-09-25T20:05:08Z", +"timestamp": 1569441908000 +}, +"page": "105013", +"update-policy": "http://dx.doi.org/10.1016/elsevier_cm_policy", +"source": "Crossref", +"is-referenced-by-count": 21, +"title": [ +"A brave new world for archaeological survey: Automated machine learning-based potsherd detection using high-resolution drone imagery" +], +"prefix": "10.1016", +"volume": "112", +"author": [ +{ +"given": "H.A.", +"family": "Orengo", +"sequence": "first", +"affiliation": [ + +] +}, +{ +"given": "A.", +"family": "Garcia-Molsosa", +"sequence": "additional", +"affiliation": [ + +] +} +], +"member": "78", +"reference": [ +{ +"key": "10.1016/j.jas.2019.105013_bib1", +"doi-asserted-by": "crossref", +"first-page": "85", +"DOI": "10.1080/17538947.2016.1250829", +"article-title": "Remote sensing heritage in a petabyte-scale: satellite data and heritage Earth Engine© applications", +"volume": "10", +"author": "Agapiou", +"year": "2017", +"journal-title": "Int. J. Digit. Earth" +}, +{ +"key": "10.1016/j.jas.2019.105013_bib2", +"series-title": "Extracting Meaning from Ploughsoil Assemblages", +"first-page": "1", +"article-title": "Extracting meaning from ploughsoil assemblages: assessments of the past, strategies for the future", +"author": "Alcock", +"year": "2000" +}, +{ +"key": "10.1016/j.jas.2019.105013_bib3", +"series-title": "Side-by-Side Survey. Comparative Regional Studies in the Mediterranean World", +"first-page": "1", +"article-title": "Introduction", +"author": "Alcock", +"year": "2004" +}, +{ +"key": "10.1016/j.jas.2019.105013_bib4", +"doi-asserted-by": "crossref", +"first-page": "93", +"DOI": "10.1111/j.1538-4632.1995.tb00338.x", +"article-title": "Local indicators of spatial association—LISA", +"volume": "27", +"author": "Anselin", +"year": "1995", +"journal-title": "Geogr. 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Computer Applications and Quantitative Methods in Archaeology", +"article-title": "Computer vision and machine learning for archaeology", +"author": "van der Maaten", +"year": "2007" +}, +{ +"key": "10.1016/j.jas.2019.105013_bib39", +"doi-asserted-by": "crossref", +"first-page": "1114", +"DOI": "10.1111/j.1475-4754.2012.00667.x", +"article-title": "Computer vision-based orthophoto mapping of complex archaeological sites: the ancient quarry of Pitaranha (Portugal-Spain)", +"volume": "54", +"author": "Verhoeven", +"year": "2012", +"journal-title": "Archaeometry" +}, +{ +"key": "10.1016/j.jas.2019.105013_bib40", +"series-title": "A Guide for Salvage Archeology", +"author": "Wendorf", +"year": "1962" +} +], +"container-title": [ +"Journal of Archaeological Science" +], +"original-title": [ + +], +"language": "en", +"link": [ +{ +"URL": "https://api.elsevier.com/content/article/PII:S0305440319301001?httpAccept=text/xml", +"content-type": "text/xml", +"content-version": "vor", +"intended-application": "text-mining" +}, +{ +"URL": "https://api.elsevier.com/content/article/PII:S0305440319301001?httpAccept=text/plain", +"content-type": "text/plain", +"content-version": "vor", +"intended-application": "text-mining" +} +], +"deposited": { +"date-parts": [ +[ +2019, +11, +25 +] +], +"date-time": "2019-11-25T06:46:34Z", +"timestamp": 1574664394000 +}, +"score": 1, +"subtitle": [ + +], +"short-title": [ + +], +"issued": { +"date-parts": [ +[ +2019, +12 +] +] +}, +"references-count": 39, +"alternative-id": [ +"S0305440319301001" +], +"URL": "http://dx.doi.org/10.1016/j.jas.2019.105013", +"relation": { + +}, +"ISSN": [ +"0305-4403" +], +"issn-type": [ +{ +"value": "0305-4403", +"type": "print" +} +], +"subject": [ +"Archaeology", +"Archaeology" +], +"published": { +"date-parts": [ +[ +2019, +12 +] +] +}, +"assertion": [ +{ +"value": "Elsevier", +"name": "publisher", +"label": "This article is maintained by" +}, +{ +"value": "A brave new world for archaeological survey: Automated machine learning-based potsherd detection using high-resolution drone imagery", +"name": "articletitle", +"label": "Article Title" +}, +{ +"value": "Journal of Archaeological Science", +"name": "journaltitle", +"label": "Journal Title" +}, +{ +"value": "https://doi.org/10.1016/j.jas.2019.105013", +"name": "articlelink", +"label": "CrossRef DOI link to publisher maintained version" +}, +{ +"value": "article", +"name": "content_type", +"label": "Content Type" +}, +{ +"value": "© 2019 The Authors. Published by Elsevier Ltd.", +"name": "copyright", +"label": "Copyright" +} +], +"article-number": "105013" +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java index 23e97a97a..392a5ab44 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/PropagationConstant.java @@ -25,6 +25,24 @@ public class PropagationConstant { private PropagationConstant() { } + public static final String DOI = "doi"; + public static final String REF_DOI = ".refs"; + + public static final String UPDATE_DATA_INFO_TYPE = "update"; + public static final String UPDATE_SUBJECT_FOS_CLASS_ID = "subject:fos"; + public static final String UPDATE_CLASS_NAME = "Inferred by OpenAIRE"; + public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip"; + + public static final String FOS_CLASS_ID = "FOS"; + public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification"; + + public static final String OPENCITATIONS_CLASSID = "sysimport:crosswalk:opencitations"; + public static final String OPENCITATIONS_CLASSNAME = "Imported from OpenCitations"; + public static final String ID_PREFIX = "50|doi_________::"; + public static final String OC_TRUST = "0.91"; + + public final static String NULL = "NULL"; + public static final String INSTITUTIONAL_REPO_TYPE = "pubsrepository::institutional"; public static final String PROPAGATION_DATA_INFO_TYPE = "propagation"; @@ -75,10 +93,25 @@ public class PropagationConstant { public static DataInfo getDataInfo( String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema) { + + return getDataInfo(inference_provenance, inference_class_id, inference_class_name, qualifierSchema, "0.85"); + } + + public static DataInfo getDataInfo( + String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema, + String trust) { + return getDataInfo( + inference_provenance, inference_class_id, inference_class_name, qualifierSchema, trust, true); + + } + + public static DataInfo getDataInfo( + String inference_provenance, String inference_class_id, String inference_class_name, String qualifierSchema, + String trust, boolean inferred) { DataInfo di = new DataInfo(); - di.setInferred(true); + di.setInferred(inferred); di.setDeletedbyinference(false); - di.setTrust("0.85"); + di.setTrust(trust); di.setInferenceprovenance(inference_provenance); di.setProvenanceaction(getQualifier(inference_class_id, inference_class_name, qualifierSchema)); return di; diff --git a/dhp-workflows/dhp-enrichment/src/site/markdown/about.md b/dhp-workflows/dhp-enrichment/src/site/markdown/about.md new file mode 100644 index 000000000..c220c63b2 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/site/markdown/about.md @@ -0,0 +1 @@ +#DHP Enrichment \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/site/site.xml b/dhp-workflows/dhp-enrichment/src/site/site.xml new file mode 100644 index 000000000..dad0cd996 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/site/site.xml @@ -0,0 +1,26 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java index 6dca09b63..61167639c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/Constants.java @@ -5,37 +5,40 @@ import java.util.Map; import com.google.common.collect.Maps; +import eu.dnetlib.dhp.schema.common.ModelConstants; + public class Constants { - public static final Map accessRightsCoarMap = Maps.newHashMap(); - public static final Map coarCodeLabelMap = Maps.newHashMap(); + protected static final Map accessRightsCoarMap = Maps.newHashMap(); + protected static final Map coarCodeLabelMap = Maps.newHashMap(); public static final String INFERRED = "Inferred by OpenAIRE"; + public static final String CABF2 = "c_abf2"; public static final String HARVESTED = "Harvested"; public static final String DEFAULT_TRUST = "0.9"; public static final String USER_CLAIM = "Linked by user"; - public static String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; + public static final String COAR_ACCESS_RIGHT_SCHEMA = "http://vocabularies.coar-repositories.org/documentation/access_rights/"; - public static String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; + public static final String ZENODO_COMMUNITY_PREFIX = "https://zenodo.org/communities/"; - public static String RESEARCH_COMMUNITY = "Research Community"; + public static final String RESEARCH_COMMUNITY = "Research Community"; - public static String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; + public static final String RESEARCH_INFRASTRUCTURE = "Research Infrastructure/Initiative"; static { - accessRightsCoarMap.put("OPEN", "c_abf2"); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_OPEN, CABF2); accessRightsCoarMap.put("RESTRICTED", "c_16ec"); - accessRightsCoarMap.put("OPEN SOURCE", "c_abf2"); - accessRightsCoarMap.put("CLOSED", "c_14cb"); - accessRightsCoarMap.put("EMBARGO", "c_f1cf"); + accessRightsCoarMap.put("OPEN SOURCE", CABF2); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_CLOSED, "c_14cb"); + accessRightsCoarMap.put(ModelConstants.ACCESS_RIGHT_EMBARGO, "c_f1cf"); } static { - coarCodeLabelMap.put("c_abf2", "OPEN"); + coarCodeLabelMap.put(CABF2, ModelConstants.ACCESS_RIGHT_OPEN); coarCodeLabelMap.put("c_16ec", "RESTRICTED"); - coarCodeLabelMap.put("c_14cb", "CLOSED"); + coarCodeLabelMap.put("c_14cb", ModelConstants.ACCESS_RIGHT_CLOSED); coarCodeLabelMap.put("c_f1cf", "EMBARGO"); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java index d20a3036e..a714cea20 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/DumpProducts.java @@ -11,12 +11,14 @@ import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; 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 eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.oaf.*; /** @@ -37,7 +39,8 @@ public class DumpProducts implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execDump(spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); + execDump( + spark, inputPath, outputPath, communityMapPath, inputClazz, outputClazz, dumpType); }); } @@ -55,7 +58,7 @@ public class DumpProducts implements Serializable { Utils .readPath(spark, inputPath, inputClazz) .map((MapFunction) value -> execMap(value, communityMap, dumpType), Encoders.bean(outputClazz)) - .filter(Objects::nonNull) + .filter((FilterFunction) value -> value != null) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") @@ -65,7 +68,7 @@ public class DumpProducts implements Serializable { private static O execMap(I value, CommunityMap communityMap, - String dumpType) { + String dumpType) throws NoAvailableEntityTypeException { Optional odInfo = Optional.ofNullable(value.getDataInfo()); if (odInfo.isPresent()) { @@ -89,11 +92,11 @@ public class DumpProducts implements Serializable { return c.getId(); } if (c.getId().contains("::") && communities.contains(c.getId().substring(0, c.getId().indexOf("::")))) { - return c.getId().substring(0, 3); + return c.getId().substring(0, c.getId().indexOf("::")); } return null; }).filter(Objects::nonNull).collect(Collectors.toList()); - if (toDumpFor.size() == 0) { + if (toDumpFor.isEmpty()) { return null; } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java index 0d2df11fe..b56849a3a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/MakeTar.java @@ -57,16 +57,16 @@ public class MakeTar implements Serializable { public static void makeTArArchive(FileSystem fileSystem, String inputPath, String outputPath, int gBperSplit) throws IOException { - RemoteIterator dir_iterator = fileSystem.listLocatedStatus(new Path(inputPath)); + RemoteIterator dirIterator = fileSystem.listLocatedStatus(new Path(inputPath)); - while (dir_iterator.hasNext()) { - LocatedFileStatus fileStatus = dir_iterator.next(); + while (dirIterator.hasNext()) { + LocatedFileStatus fileStatus = dirIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - String entity = p_string.substring(p_string.lastIndexOf("/") + 1); + String pathString = p.toString(); + String entity = pathString.substring(pathString.lastIndexOf("/") + 1); - MakeTarArchive.tarMaxSize(fileSystem, p_string, outputPath + "/" + entity, entity, gBperSplit); + MakeTarArchive.tarMaxSize(fileSystem, pathString, outputPath + "/" + entity, entity, gBperSplit); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java index dc740e811..b972de6e9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystem.java @@ -18,10 +18,10 @@ public class QueryInformationSystem { private ISLookUpService isLookUp; - private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + private static final String XQUERY_ALL = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + " and ($x//context/param[./@name = 'status']/text() = 'all') " + " return " + " " + @@ -29,9 +29,22 @@ public class QueryInformationSystem { "{$x//CONFIGURATION/context/@label}" + ""; - public CommunityMap getCommunityMap() + private static final String XQUERY_CI = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + + + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + + " and $x//CONFIGURATION/context[./@id=%s] " + + + " return " + + " " + + "{$x//CONFIGURATION/context/@id}" + + "{$x//CONFIGURATION/context/@label}" + + ""; + + public CommunityMap getCommunityMap(boolean singleCommunity, String communityId) throws ISLookUpException, DocumentException, SAXException { - return getMap(isLookUp.quickSearchProfile(XQUERY)); + if (singleCommunity) + return getMap(isLookUp.quickSearchProfile(XQUERY_CI.replace("%s", "'" + communityId + "'"))); + return getMap(isLookUp.quickSearchProfile(XQUERY_ALL)); } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java index 500fe5986..1beea5cb4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/ResultMapper.java @@ -7,21 +7,28 @@ import java.util.stream.Collectors; import org.apache.commons.lang3.StringUtils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.*; +import eu.dnetlib.dhp.schema.dump.oaf.AccessRight; +import eu.dnetlib.dhp.schema.dump.oaf.Author; +import eu.dnetlib.dhp.schema.dump.oaf.Country; +import eu.dnetlib.dhp.schema.dump.oaf.GeoLocation; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.KeyValue; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.Qualifier; +import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityInstance; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Context; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; -import eu.dnetlib.dhp.schema.oaf.DataInfo; -import eu.dnetlib.dhp.schema.oaf.Field; -import eu.dnetlib.dhp.schema.oaf.Journal; -import eu.dnetlib.dhp.schema.oaf.StructuredProperty; +import eu.dnetlib.dhp.schema.oaf.*; public class ResultMapper implements Serializable { public static Result map( - E in, Map communityMap, String dumpType) { + E in, Map communityMap, String dumpType) throws NoAvailableEntityTypeException { Result out; if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { @@ -33,113 +40,19 @@ public class ResultMapper implements Serializable { eu.dnetlib.dhp.schema.oaf.Result input = (eu.dnetlib.dhp.schema.oaf.Result) in; Optional ort = Optional.ofNullable(input.getResulttype()); if (ort.isPresent()) { - switch (ort.get().getClassid()) { - case "publication": - Optional journal = Optional - .ofNullable(((eu.dnetlib.dhp.schema.oaf.Publication) input).getJournal()); - if (journal.isPresent()) { - Journal j = journal.get(); - Container c = new Container(); - c.setConferencedate(j.getConferencedate()); - c.setConferenceplace(j.getConferenceplace()); - c.setEdition(j.getEdition()); - c.setEp(j.getEp()); - c.setIss(j.getIss()); - c.setIssnLinking(j.getIssnLinking()); - c.setIssnOnline(j.getIssnOnline()); - c.setIssnPrinted(j.getIssnPrinted()); - c.setName(j.getName()); - c.setSp(j.getSp()); - c.setVol(j.getVol()); - out.setContainer(c); - out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); - } - break; - case "dataset": - eu.dnetlib.dhp.schema.oaf.Dataset id = (eu.dnetlib.dhp.schema.oaf.Dataset) input; - Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); - Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + try { - out - .setGeolocation( - Optional - .ofNullable(id.getGeolocation()) - .map( - igl -> igl - .stream() - .filter(Objects::nonNull) - .map(gli -> { - GeoLocation gl = new GeoLocation(); - gl.setBox(gli.getBox()); - gl.setPlace(gli.getPlace()); - gl.setPoint(gli.getPoint()); - return gl; - }) - .collect(Collectors.toList())) - .orElse(null)); + addTypeSpecificInformation(out, input, ort); - out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); - break; - case "software": + Optional + .ofNullable(input.getAuthor()) + .ifPresent( + ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); - eu.dnetlib.dhp.schema.oaf.Software is = (eu.dnetlib.dhp.schema.oaf.Software) input; - Optional - .ofNullable(is.getCodeRepositoryUrl()) - .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); - Optional - .ofNullable(is.getDocumentationUrl()) - .ifPresent( - value -> out - .setDocumentationUrl( - value - .stream() - .map(Field::getValue) - .collect(Collectors.toList()))); + // I do not map Access Right UNKNOWN or OTHER - Optional - .ofNullable(is.getProgrammingLanguage()) - .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); - - out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); - break; - case "other": - - eu.dnetlib.dhp.schema.oaf.OtherResearchProduct ir = (eu.dnetlib.dhp.schema.oaf.OtherResearchProduct) input; - out - .setContactgroup( - Optional - .ofNullable(ir.getContactgroup()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out - .setContactperson( - Optional - .ofNullable(ir.getContactperson()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - out - .setTool( - Optional - .ofNullable(ir.getTool()) - .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) - .orElse(null)); - - out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); - - break; - } - - Optional - .ofNullable(input.getAuthor()) - .ifPresent( - ats -> out.setAuthor(ats.stream().map(ResultMapper::getAuthor).collect(Collectors.toList()))); - - // I do not map Access Right UNKNOWN or OTHER - - Optional oar = Optional.ofNullable(input.getBestaccessright()); - if (oar.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { + Optional oar = Optional.ofNullable(input.getBestaccessright()); + if (oar.isPresent() && Constants.accessRightsCoarMap.containsKey(oar.get().getClassid())) { String code = Constants.accessRightsCoarMap.get(oar.get().getClassid()); out .setBestaccessright( @@ -149,226 +62,340 @@ public class ResultMapper implements Serializable { Constants.coarCodeLabelMap.get(code), Constants.COAR_ACCESS_RIGHT_SCHEMA)); } - } - final List contributorList = new ArrayList<>(); - Optional - .ofNullable(input.getContributor()) - .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); - out.setContributor(contributorList); + final List contributorList = new ArrayList<>(); + Optional + .ofNullable(input.getContributor()) + .ifPresent(value -> value.stream().forEach(c -> contributorList.add(c.getValue()))); + out.setContributor(contributorList); - Optional - .ofNullable(input.getCountry()) - .ifPresent( - value -> out - .setCountry( - value - .stream() - .map( - c -> { - if (c.getClassid().equals((ModelConstants.UNKNOWN))) { - return null; - } - Country country = new Country(); - country.setCode(c.getClassid()); - country.setLabel(c.getClassname()); - Optional - .ofNullable(c.getDataInfo()) - .ifPresent( - provenance -> country - .setProvenance( - Provenance - .newInstance( - provenance - .getProvenanceaction() - .getClassname(), - c.getDataInfo().getTrust()))); - return country; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList()))); - - final List coverageList = new ArrayList<>(); - Optional - .ofNullable(input.getCoverage()) - .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); - out.setCoverage(coverageList); - - out.setDateofcollection(input.getDateofcollection()); - - final List descriptionList = new ArrayList<>(); - Optional - .ofNullable(input.getDescription()) - .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); - out.setDescription(descriptionList); - Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); - if (oStr.isPresent()) { - out.setEmbargoenddate(oStr.get().getValue()); - } - - final List formatList = new ArrayList<>(); - Optional - .ofNullable(input.getFormat()) - .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); - out.setFormat(formatList); - out.setId(input.getId()); - out.setOriginalId(input.getOriginalId()); - - Optional> oInst = Optional - .ofNullable(input.getInstance()); - - if (oInst.isPresent()) { - if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((GraphResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); - } else { - ((CommunityResult) out) - .setInstance( - oInst.get().stream().map(ResultMapper::getCommunityInstance).collect(Collectors.toList())); - } - } - - Optional oL = Optional.ofNullable(input.getLanguage()); - if (oL.isPresent()) { - eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); - out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); - } - Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); - if (oLong.isPresent()) { - out.setLastupdatetimestamp(oLong.get()); - } - Optional> otitle = Optional.ofNullable(input.getTitle()); - if (otitle.isPresent()) { - List iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) - .collect(Collectors.toList()); - if (iTitle.size() > 0) { - out.setMaintitle(iTitle.get(0).getValue()); - } - - iTitle = otitle - .get() - .stream() - .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) - .collect(Collectors.toList()); - if (iTitle.size() > 0) { - out.setSubtitle(iTitle.get(0).getValue()); - } - - } - - List pids = new ArrayList<>(); - Optional - .ofNullable(input.getPid()) - .ifPresent( - value -> value - .stream() - .forEach( - p -> pids - .add( - ControlledField - .newInstance(p.getQualifier().getClassid(), p.getValue())))); - out.setPid(pids); - oStr = Optional.ofNullable(input.getDateofacceptance()); - if (oStr.isPresent()) { - out.setPublicationdate(oStr.get().getValue()); - } - oStr = Optional.ofNullable(input.getPublisher()); - if (oStr.isPresent()) { - out.setPublisher(oStr.get().getValue()); - } - - List sourceList = new ArrayList<>(); - Optional - .ofNullable(input.getSource()) - .ifPresent(value -> value.stream().forEach(s -> sourceList.add(s.getValue()))); - // out.setSource(input.getSource().stream().map(s -> s.getValue()).collect(Collectors.toList())); - List subjectList = new ArrayList<>(); - Optional - .ofNullable(input.getSubject()) - .ifPresent( - value -> value - .forEach(s -> subjectList.add(getSubject(s)))); - - out.setSubjects(subjectList); - - out.setType(input.getResulttype().getClassid()); - } - - if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { - ((CommunityResult) out) - .setCollectedfrom( - input - .getCollectedfrom() - .stream() - .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) - .collect(Collectors.toList())); - - Set communities = communityMap.keySet(); - List contextList = Optional - .ofNullable( - input - .getContext()) - .map( - value -> value - .stream() - .map(c -> { - String community_id = c.getId(); - if (community_id.indexOf("::") > 0) { - community_id = community_id.substring(0, community_id.indexOf("::")); - } - if (communities.contains(community_id)) { - Context context = new Context(); - context.setCode(community_id); - context.setLabel(communityMap.get(community_id)); - Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); - if (dataInfo.isPresent()) { - List provenance = new ArrayList<>(); - provenance - .addAll( - dataInfo - .get() - .stream() - .map( - di -> Optional - .ofNullable(di.getProvenanceaction()) - .map( - provenanceaction -> Provenance + Optional + .ofNullable(input.getCountry()) + .ifPresent( + value -> out + .setCountry( + value + .stream() + .map( + c -> { + if (c.getClassid().equals((ModelConstants.UNKNOWN))) { + return null; + } + Country country = new Country(); + country.setCode(c.getClassid()); + country.setLabel(c.getClassname()); + Optional + .ofNullable(c.getDataInfo()) + .ifPresent( + provenance -> country + .setProvenance( + Provenance .newInstance( - provenanceaction.getClassname(), di.getTrust())) - .orElse(null)) - .filter(Objects::nonNull) - .collect(Collectors.toSet())); + provenance + .getProvenanceaction() + .getClassname(), + c.getDataInfo().getTrust()))); + return country; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList()))); - context.setProvenance(getUniqueProvenance(provenance)); - } - return context; - } - return null; - }) - .filter(Objects::nonNull) - .collect(Collectors.toList())) - .orElse(new ArrayList<>()); + final List coverageList = new ArrayList<>(); + Optional + .ofNullable(input.getCoverage()) + .ifPresent(value -> value.stream().forEach(c -> coverageList.add(c.getValue()))); + out.setCoverage(coverageList); - if (contextList.size() > 0) { - Set hashValue = new HashSet<>(); - List remainigContext = new ArrayList<>(); - contextList.forEach(c -> { - if (!hashValue.contains(c.hashCode())) { - remainigContext.add(c); - hashValue.add(c.hashCode()); + out.setDateofcollection(input.getDateofcollection()); + + final List descriptionList = new ArrayList<>(); + Optional + .ofNullable(input.getDescription()) + .ifPresent(value -> value.forEach(d -> descriptionList.add(d.getValue()))); + out.setDescription(descriptionList); + Optional> oStr = Optional.ofNullable(input.getEmbargoenddate()); + if (oStr.isPresent()) { + out.setEmbargoenddate(oStr.get().getValue()); + } + + final List formatList = new ArrayList<>(); + Optional + .ofNullable(input.getFormat()) + .ifPresent(value -> value.stream().forEach(f -> formatList.add(f.getValue()))); + out.setFormat(formatList); + out.setId(input.getId()); + out.setOriginalId(input.getOriginalId()); + + Optional> oInst = Optional + .ofNullable(input.getInstance()); + + if (oInst.isPresent()) { + if (Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { + ((GraphResult) out) + .setInstance( + oInst.get().stream().map(ResultMapper::getGraphInstance).collect(Collectors.toList())); + } else { + ((CommunityResult) out) + .setInstance( + oInst + .get() + .stream() + .map(ResultMapper::getCommunityInstance) + .collect(Collectors.toList())); } - }); - ((CommunityResult) out).setContext(remainigContext); + } + + Optional oL = Optional.ofNullable(input.getLanguage()); + if (oL.isPresent()) { + eu.dnetlib.dhp.schema.oaf.Qualifier language = oL.get(); + out.setLanguage(Qualifier.newInstance(language.getClassid(), language.getClassname())); + } + Optional oLong = Optional.ofNullable(input.getLastupdatetimestamp()); + if (oLong.isPresent()) { + out.setLastupdatetimestamp(oLong.get()); + } + Optional> otitle = Optional.ofNullable(input.getTitle()); + if (otitle.isPresent()) { + List iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("main title")) + .collect(Collectors.toList()); + if (!iTitle.isEmpty()) { + out.setMaintitle(iTitle.get(0).getValue()); + } + + iTitle = otitle + .get() + .stream() + .filter(t -> t.getQualifier().getClassid().equalsIgnoreCase("subtitle")) + .collect(Collectors.toList()); + if (!iTitle.isEmpty()) { + out.setSubtitle(iTitle.get(0).getValue()); + } + + } + + Optional + .ofNullable(input.getPid()) + .ifPresent( + value -> out + .setPid( + value + .stream() + .map( + p -> ControlledField + .newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + + oStr = Optional.ofNullable(input.getDateofacceptance()); + if (oStr.isPresent()) { + out.setPublicationdate(oStr.get().getValue()); + } + oStr = Optional.ofNullable(input.getPublisher()); + if (oStr.isPresent()) { + out.setPublisher(oStr.get().getValue()); + } + + Optional + .ofNullable(input.getSource()) + .ifPresent( + value -> out.setSource(value.stream().map(Field::getValue).collect(Collectors.toList()))); + + List subjectList = new ArrayList<>(); + Optional + .ofNullable(input.getSubject()) + .ifPresent( + value -> value + .forEach(s -> subjectList.add(getSubject(s)))); + + out.setSubjects(subjectList); + + out.setType(input.getResulttype().getClassid()); + + if (!Constants.DUMPTYPE.COMPLETE.getType().equals(dumpType)) { + ((CommunityResult) out) + .setCollectedfrom( + input + .getCollectedfrom() + .stream() + .map(cf -> KeyValue.newInstance(cf.getKey(), cf.getValue())) + .collect(Collectors.toList())); + + Set communities = communityMap.keySet(); + List contextList = Optional + .ofNullable( + input + .getContext()) + .map( + value -> value + .stream() + .map(c -> { + String communityId = c.getId(); + if (communityId.contains("::")) { + communityId = communityId.substring(0, communityId.indexOf("::")); + } + if (communities.contains(communityId)) { + Context context = new Context(); + context.setCode(communityId); + context.setLabel(communityMap.get(communityId)); + Optional> dataInfo = Optional.ofNullable(c.getDataInfo()); + if (dataInfo.isPresent()) { + List provenance = new ArrayList<>(); + provenance + .addAll( + dataInfo + .get() + .stream() + .map( + di -> Optional + .ofNullable(di.getProvenanceaction()) + .map( + provenanceaction -> Provenance + .newInstance( + provenanceaction.getClassname(), + di.getTrust())) + .orElse(null)) + .filter(Objects::nonNull) + .collect(Collectors.toSet())); + + try { + context.setProvenance(getUniqueProvenance(provenance)); + } catch (NoAvailableEntityTypeException e) { + e.printStackTrace(); + } + } + return context; + } + return null; + }) + .filter(Objects::nonNull) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); + + if (!contextList.isEmpty()) { + Set hashValue = new HashSet<>(); + List remainigContext = new ArrayList<>(); + contextList.forEach(c -> { + if (!hashValue.contains(c.hashCode())) { + remainigContext.add(c); + hashValue.add(c.hashCode()); + } + }); + ((CommunityResult) out).setContext(remainigContext); + } + } + } catch (ClassCastException cce) { + return out; } } + return out; } + private static void addTypeSpecificInformation(Result out, eu.dnetlib.dhp.schema.oaf.Result input, + Optional ort) throws NoAvailableEntityTypeException { + switch (ort.get().getClassid()) { + case "publication": + Optional journal = Optional + .ofNullable(((Publication) input).getJournal()); + if (journal.isPresent()) { + Journal j = journal.get(); + Container c = new Container(); + c.setConferencedate(j.getConferencedate()); + c.setConferenceplace(j.getConferenceplace()); + c.setEdition(j.getEdition()); + c.setEp(j.getEp()); + c.setIss(j.getIss()); + c.setIssnLinking(j.getIssnLinking()); + c.setIssnOnline(j.getIssnOnline()); + c.setIssnPrinted(j.getIssnPrinted()); + c.setName(j.getName()); + c.setSp(j.getSp()); + c.setVol(j.getVol()); + out.setContainer(c); + out.setType(ModelConstants.PUBLICATION_DEFAULT_RESULTTYPE.getClassname()); + } + break; + case "dataset": + Dataset id = (Dataset) input; + Optional.ofNullable(id.getSize()).ifPresent(v -> out.setSize(v.getValue())); + Optional.ofNullable(id.getVersion()).ifPresent(v -> out.setVersion(v.getValue())); + + out + .setGeolocation( + Optional + .ofNullable(id.getGeolocation()) + .map( + igl -> igl + .stream() + .filter(Objects::nonNull) + .map(gli -> { + GeoLocation gl = new GeoLocation(); + gl.setBox(gli.getBox()); + gl.setPlace(gli.getPlace()); + gl.setPoint(gli.getPoint()); + return gl; + }) + .collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.DATASET_DEFAULT_RESULTTYPE.getClassname()); + break; + case "software": + + Software is = (Software) input; + Optional + .ofNullable(is.getCodeRepositoryUrl()) + .ifPresent(value -> out.setCodeRepositoryUrl(value.getValue())); + Optional + .ofNullable(is.getDocumentationUrl()) + .ifPresent( + value -> out + .setDocumentationUrl( + value + .stream() + .map(Field::getValue) + .collect(Collectors.toList()))); + + Optional + .ofNullable(is.getProgrammingLanguage()) + .ifPresent(value -> out.setProgrammingLanguage(value.getClassid())); + + out.setType(ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE.getClassname()); + break; + case "other": + + OtherResearchProduct ir = (OtherResearchProduct) input; + out + .setContactgroup( + Optional + .ofNullable(ir.getContactgroup()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + + out + .setContactperson( + Optional + .ofNullable(ir.getContactperson()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + out + .setTool( + Optional + .ofNullable(ir.getTool()) + .map(value -> value.stream().map(Field::getValue).collect(Collectors.toList())) + .orElse(null)); + + out.setType(ModelConstants.ORP_DEFAULT_RESULTTYPE.getClassname()); + + break; + default: + throw new NoAvailableEntityTypeException(); + } + } + private static Instance getGraphInstance(eu.dnetlib.dhp.schema.oaf.Instance i) { Instance instance = new Instance(); @@ -397,21 +424,58 @@ public class ResultMapper implements Serializable { } private static void setCommonValue(eu.dnetlib.dhp.schema.oaf.Instance i, I instance) { - Optional opAr = Optional - .ofNullable(i.getAccessright()); - if (opAr.isPresent()) { - if (Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { - String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); - instance - .setAccessright( - AccessRight - .newInstance( - code, - Constants.coarCodeLabelMap.get(code), - Constants.COAR_ACCESS_RIGHT_SCHEMA)); + Optional opAr = Optional.ofNullable(i.getAccessright()); + + if (opAr.isPresent() && Constants.accessRightsCoarMap.containsKey(opAr.get().getClassid())) { + String code = Constants.accessRightsCoarMap.get(opAr.get().getClassid()); + + instance + .setAccessright( + AccessRight + .newInstance( + code, + Constants.coarCodeLabelMap.get(code), + Constants.COAR_ACCESS_RIGHT_SCHEMA)); + if (opAr.get().getOpenAccessRoute() != null) { + switch (opAr.get().getOpenAccessRoute()) { + case hybrid: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.hybrid); + break; + case gold: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.gold); + break; + case green: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.green); + break; + case bronze: + instance.getAccessright().setOpenAccessRoute(OpenAccessRoute.bronze); + break; + + } } + } + Optional + .ofNullable(i.getPid()) + .ifPresent( + pid -> instance + .setPid( + pid + .stream() + .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + + Optional + .ofNullable(i.getAlternateIdentifier()) + .ifPresent( + ai -> instance + .setAlternateIdentifier( + ai + .stream() + .map(p -> ControlledField.newInstance(p.getQualifier().getClassid(), p.getValue())) + .collect(Collectors.toList()))); + Optional .ofNullable(i.getLicense()) .ifPresent(value -> instance.setLicense(value.getValue())); @@ -424,11 +488,26 @@ public class ResultMapper implements Serializable { Optional .ofNullable(i.getInstancetype()) .ifPresent(value -> instance.setType(value.getClassname())); + Optional.ofNullable(i.getUrl()).ifPresent(value -> instance.setUrl(value)); + Optional> oPca = Optional.ofNullable(i.getProcessingchargeamount()); + Optional> oPcc = Optional.ofNullable(i.getProcessingchargecurrency()); + if (oPca.isPresent() && oPcc.isPresent()) { + Field pca = oPca.get(); + Field pcc = oPcc.get(); + if (!pca.getValue().trim().equals("") && !pcc.getValue().trim().equals("")) { + APC apc = new APC(); + apc.setCurrency(oPcc.get().getValue()); + apc.setAmount(oPca.get().getValue()); + instance.setArticleprocessingcharge(apc); + } + + } Optional.ofNullable(i.getUrl()).ifPresent(instance::setUrl); } - private static List getUniqueProvenance(List provenance) { + private static List getUniqueProvenance(List provenance) + throws NoAvailableEntityTypeException { Provenance iProv = new Provenance(); Provenance hProv = new Provenance(); @@ -450,6 +529,8 @@ public class ResultMapper implements Serializable { case Constants.USER_CLAIM: lProv = getHighestTrust(lProv, p); break; + default: + throw new NoAvailableEntityTypeException(); } } @@ -503,34 +584,67 @@ public class ResultMapper implements Serializable { return a; } - private static Pid getOrcid(List p) { - for (StructuredProperty pid : p) { - if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID)) { - Optional di = Optional.ofNullable(pid.getDataInfo()); - if (di.isPresent()) { - return Pid + private static Pid getAuthorPid(StructuredProperty pid) { + Optional di = Optional.ofNullable(pid.getDataInfo()); + if (di.isPresent()) { + return Pid + .newInstance( + ControlledField .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()), - Provenance - .newInstance( - di.get().getProvenanceaction().getClassname(), - di.get().getTrust())); - } else { - return Pid + pid.getQualifier().getClassid(), + pid.getValue()), + Provenance .newInstance( - ControlledField - .newInstance( - pid.getQualifier().getClassid(), - pid.getValue()) + di.get().getProvenanceaction().getClassname(), + di.get().getTrust())); + } else { + return Pid + .newInstance( + ControlledField + .newInstance( + pid.getQualifier().getClassid(), + pid.getValue()) - ); - } - - } + ); } + } + + private static Pid getOrcid(List p) { + List pidList = p.stream().map(pid -> { + if (pid.getQualifier().getClassid().equals(ModelConstants.ORCID) || + (pid.getQualifier().getClassid().equals(ModelConstants.ORCID_PENDING))) { + return pid; + } + return null; + }).filter(Objects::nonNull).collect(Collectors.toList()); + + if (pidList.size() == 1) { + return getAuthorPid(pidList.get(0)); + } + + List orcid = pidList + .stream() + .filter( + ap -> ap + .getQualifier() + .getClassid() + .equals(ModelConstants.ORCID)) + .collect(Collectors.toList()); + if (orcid.size() == 1) { + return getAuthorPid(orcid.get(0)); + } + orcid = pidList + .stream() + .filter( + ap -> ap + .getQualifier() + .getClassid() + .equals(ModelConstants.ORCID_PENDING)) + .collect(Collectors.toList()); + if (orcid.size() == 1) { + return getAuthorPid(orcid.get(0)); + } + return null; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java index f86f6918f..a6595d756 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SaveCommunityMap.java @@ -6,6 +6,7 @@ import java.io.IOException; import java.io.OutputStreamWriter; import java.io.Serializable; import java.nio.charset.StandardCharsets; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.hadoop.conf.Configuration; @@ -18,6 +19,7 @@ import org.slf4j.LoggerFactory; import org.xml.sax.SAXException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; /** @@ -30,9 +32,9 @@ import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; public class SaveCommunityMap implements Serializable { private static final Logger log = LoggerFactory.getLogger(SaveCommunityMap.class); - private final QueryInformationSystem queryInformationSystem; + private final transient QueryInformationSystem queryInformationSystem; - private final BufferedWriter writer; + private final transient BufferedWriter writer; public SaveCommunityMap(String hdfsPath, String hdfsNameNode, String isLookUpUrl) throws IOException { final Configuration conf = new Configuration(); @@ -70,13 +72,28 @@ public class SaveCommunityMap implements Serializable { final String isLookUpUrl = parser.get("isLookUpUrl"); log.info("isLookUpUrl: {}", isLookUpUrl); + final Boolean singleCommunity = Optional + .ofNullable(parser.get("singleDeposition")) + .map(Boolean::valueOf) + .orElse(false); + + final String community_id = Optional.ofNullable(parser.get("communityId")).orElse(null); + final SaveCommunityMap scm = new SaveCommunityMap(outputPath, nameNode, isLookUpUrl); - scm.saveCommunityMap(); + scm.saveCommunityMap(singleCommunity, community_id); + } - private void saveCommunityMap() throws ISLookUpException, IOException, DocumentException, SAXException { - writer.write(Utils.OBJECT_MAPPER.writeValueAsString(queryInformationSystem.getCommunityMap())); + private void saveCommunityMap(boolean singleCommunity, String communityId) + throws ISLookUpException, IOException, DocumentException, SAXException { + final String communityMapString = Utils.OBJECT_MAPPER + .writeValueAsString(queryInformationSystem.getCommunityMap(singleCommunity, communityId)); + log.info("communityMap {} ", communityMapString); + writer + .write( + communityMapString); writer.close(); } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java index ba26b708a..a19a3a5b6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/SendToZenodoHDFS.java @@ -5,15 +5,13 @@ import java.io.Serializable; import java.util.Optional; import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.*; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.common.api.MissingConceptDoiException; import eu.dnetlib.dhp.common.api.ZenodoAPIClient; -import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; public class SendToZenodoHDFS implements Serializable { @@ -21,8 +19,6 @@ public class SendToZenodoHDFS implements Serializable { private static final String VERSION = "version"; // to be used to upload a new version of a published deposition private static final String UPDATE = "update"; // to upload content to an open deposition not published - private static final Log log = LogFactory.getLog(SendToZenodoHDFS.class); - public static void main(final String[] args) throws Exception, MissingConceptDoiException { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils @@ -48,15 +44,12 @@ public class SendToZenodoHDFS implements Serializable { .orElse(false); final String depositionId = Optional.ofNullable(parser.get("depositionId")).orElse(null); - final String communityMapPath = parser.get("communityMapPath"); Configuration conf = new Configuration(); conf.set("fs.defaultFS", hdfsNameNode); FileSystem fileSystem = FileSystem.get(conf); - CommunityMap communityMap = Utils.readCommunityMap(fileSystem, communityMapPath); - RemoteIterator fileStatusListIterator = fileSystem .listFiles( new Path(hdfsPath), true); @@ -77,19 +70,17 @@ public class SendToZenodoHDFS implements Serializable { } zenodoApiClient.uploadOpenDeposition(depositionId); break; + default: + throw new NoAvailableEntityTypeException(); } while (fileStatusListIterator.hasNext()) { LocatedFileStatus fileStatus = fileStatusListIterator.next(); Path p = fileStatus.getPath(); - String p_string = p.toString(); - if (!p_string.endsWith("_SUCCESS")) { - String name = p_string.substring(p_string.lastIndexOf("/") + 1); - log.info("Sending information for community: " + name); - if (communityMap.containsKey(name.substring(0, name.lastIndexOf(".")))) { - name = communityMap.get(name.substring(0, name.lastIndexOf("."))).replace(" ", "_") + ".tar"; - } + String pString = p.toString(); + if (!pString.endsWith("_SUCCESS")) { + String name = pString.substring(pString.lastIndexOf("/") + 1); FSDataInputStream inputStream = fileSystem.open(p); zenodoApiClient.uploadIS(inputStream, name, fileStatus.getLen()); @@ -101,7 +92,7 @@ public class SendToZenodoHDFS implements Serializable { zenodoApiClient.sendMretadata(metadata); } - if (publish) { + if (Boolean.TRUE.equals(publish)) { zenodoApiClient.publish(); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java index b92eb3e60..ee6341f84 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/CommunitySplit.java @@ -4,9 +4,7 @@ package eu.dnetlib.dhp.oa.graph.dump.community; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; -import java.util.NoSuchElementException; import java.util.Optional; -import java.util.Set; import java.util.stream.Collectors; import org.apache.spark.SparkConf; @@ -17,6 +15,7 @@ import org.apache.spark.sql.SparkSession; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Context; /** * This class splits the dumped results according to the research community - research initiative/infrastructure they @@ -35,12 +34,13 @@ public class CommunitySplit implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - execSplit(spark, inputPath, outputPath, Utils.getCommunityMap(spark, communityMapPath).keySet()); + CommunityMap communityMap = Utils.getCommunityMap(spark, communityMapPath); + execSplit(spark, inputPath, outputPath, communityMap); }); } private static void execSplit(SparkSession spark, String inputPath, String outputPath, - Set communities) { + CommunityMap communities) { Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -49,34 +49,32 @@ public class CommunitySplit implements Serializable { .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); communities - .forEach(c -> printResult(c, result, outputPath)); + .keySet() + .stream() + .forEach(c -> printResult(c, result, outputPath + "/" + communities.get(c).replace(" ", "_"))); } - private static void printResult(String community, Dataset result, String outputPath) { + private static void printResult(String c, Dataset result, String outputPath) { Dataset communityProducts = result - .filter((FilterFunction) r -> containsCommunity(r, community)); + .filter((FilterFunction) r -> containsCommunity(r, c)); + + communityProducts + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); - try { - communityProducts.first(); - communityProducts - .write() - .option("compression", "gzip") - .mode(SaveMode.Overwrite) - .json(outputPath + "/" + community); - } catch (NoSuchElementException e) { - // ignoring it on purpose - } } - private static boolean containsCommunity(CommunityResult r, String community) { + private static boolean containsCommunity(CommunityResult r, String c) { if (Optional.ofNullable(r.getContext()).isPresent()) { - return !r + return r .getContext() .stream() - .filter(con -> con.getCode().equals(community)) + .map(Context::getCode) .collect(Collectors.toList()) - .isEmpty(); + .contains(c); } return false; } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java index 0f2b4c2ed..87ac20948 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/community/SparkPrepareResultProject.java @@ -26,9 +26,11 @@ import org.xml.sax.SAXException; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.Provenance; import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; +import eu.dnetlib.dhp.schema.dump.oaf.community.Validated; import eu.dnetlib.dhp.schema.oaf.DataInfo; import eu.dnetlib.dhp.schema.oaf.Field; import eu.dnetlib.dhp.schema.oaf.Relation; @@ -78,7 +80,9 @@ public class SparkPrepareResultProject implements Serializable { private static void prepareResultProjectList(SparkSession spark, String inputPath, String outputPath) { Dataset relation = Utils .readPath(spark, inputPath + "/relation", Relation.class) - .filter("dataInfo.deletedbyinference = false and lower(relClass) = 'isproducedby'"); + .filter( + "dataInfo.deletedbyinference = false and lower(relClass) = '" + + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); Dataset projects = Utils .readPath(spark, inputPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); @@ -98,7 +102,7 @@ public class SparkPrepareResultProject implements Serializable { rp.setResultId(s); eu.dnetlib.dhp.schema.oaf.Project p = first._1(); projectSet.add(p.getId()); - Project ps = getProject(p); + Project ps = getProject(p, first._2); List projList = new ArrayList<>(); projList.add(ps); @@ -107,7 +111,7 @@ public class SparkPrepareResultProject implements Serializable { eu.dnetlib.dhp.schema.oaf.Project op = c._1(); if (!projectSet.contains(op.getId())) { projList - .add(getProject(op)); + .add(getProject(op, c._2)); projectSet.add(op.getId()); @@ -122,7 +126,7 @@ public class SparkPrepareResultProject implements Serializable { .json(outputPath); } - private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op) { + private static Project getProject(eu.dnetlib.dhp.schema.oaf.Project op, Relation relation) { Project p = Project .newInstance( op.getId(), @@ -157,7 +161,9 @@ public class SparkPrepareResultProject implements Serializable { provenance.setTrust(di.get().getTrust()); p.setProvenance(provenance); } - + if (Boolean.TRUE.equals(relation.getValidated())) { + p.setValidated(Validated.newInstance(relation.getValidated(), relation.getValidationDate())); + } return p; } @@ -173,8 +179,8 @@ public class SparkPrepareResultProject implements Serializable { f.setName(((Node) (doc.selectNodes("//funder/name").get(0))).getText()); f.setJurisdiction(((Node) (doc.selectNodes("//funder/jurisdiction").get(0))).getText()); for (Object o : doc.selectNodes("//funding_level_0")) { - List node = ((Node) o).selectNodes("./name"); - f.setFundingStream(((Node) node.get(0)).getText()); + List node = ((Node) o).selectNodes("./name"); + f.setFundingStream((node.get(0)).getText()); } return f; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java index 10f2014d0..a468e334d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateContextRelation.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.graph.*; import eu.dnetlib.dhp.schema.oaf.Datasource; @@ -38,6 +39,7 @@ public class CreateContextRelation implements Serializable { private final transient QueryInformationSystem queryInformationSystem; private static final String CONTEX_RELATION_DATASOURCE = "contentproviders"; + private static final String CONTEX_RELATION_PROJECT = "projects"; public static void main(String[] args) throws Exception { String jsonConfiguration = IOUtils @@ -72,6 +74,10 @@ public class CreateContextRelation implements Serializable { cce.execute(Process::getRelation, CONTEX_RELATION_DATASOURCE, ModelSupport.getIdPrefix(Datasource.class)); log.info("Creating relations for projects... "); + cce + .execute( + Process::getRelation, CONTEX_RELATION_PROJECT, + ModelSupport.getIdPrefix(eu.dnetlib.dhp.schema.oaf.Project.class)); cce.close(); @@ -115,7 +121,7 @@ public class CreateContextRelation implements Serializable { writer.write(Utils.OBJECT_MAPPER.writeValueAsString(r)); writer.newLine(); } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java index 36ced3a4a..7f64db41c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpGraphEntities.java @@ -1,6 +1,7 @@ package eu.dnetlib.dhp.oa.graph.dump.complete; +import static com.jayway.jsonpath.Filter.filter; import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.io.Serializable; @@ -9,7 +10,10 @@ import java.util.*; import java.util.stream.Collectors; import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.SaveMode; import org.apache.spark.sql.SparkSession; @@ -18,6 +22,8 @@ import org.dom4j.DocumentException; import org.dom4j.Node; import org.dom4j.io.SAXReader; +import com.fasterxml.jackson.databind.ObjectMapper; + import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.common.ModelSupport; @@ -453,13 +459,17 @@ public class DumpGraphEntities implements Serializable { .map( (MapFunction) o -> mapOrganization((eu.dnetlib.dhp.schema.oaf.Organization) o), Encoders.bean(Organization.class)) + .filter((FilterFunction) o -> o != null) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath); } - private static Organization mapOrganization(eu.dnetlib.dhp.schema.oaf.Organization org) { + private static eu.dnetlib.dhp.schema.dump.oaf.graph.Organization mapOrganization( + eu.dnetlib.dhp.schema.oaf.Organization org) { + if (org.getDataInfo().getDeletedbyinference()) + return null; Organization organization = new Organization(); Optional diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java index 31886d1b1..3e47ee664 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Extractor.java @@ -62,22 +62,7 @@ public class Extractor implements Serializable { .readPath(spark, inputPath, inputClazz) .flatMap((FlatMapFunction) value -> { List relationList = new ArrayList<>(); - Optional - .ofNullable(value.getInstance()) - .ifPresent(inst -> inst.forEach(instance -> { - Optional - .ofNullable(instance.getCollectedfrom()) - .ifPresent( - cf -> getRelatioPair( - value, relationList, cf, - ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); - Optional - .ofNullable(instance.getHostedby()) - .ifPresent( - hb -> getRelatioPair( - value, relationList, hb, - Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); - })); + extractRelationsFromInstance(hashCodes, value, relationList); Set communities = communityMap.keySet(); Optional .ofNullable(value.getContext()) @@ -136,8 +121,28 @@ public class Extractor implements Serializable { } + private void extractRelationsFromInstance(Set hashCodes, R value, + List relationList) { + Optional + .ofNullable(value.getInstance()) + .ifPresent(inst -> inst.forEach(instance -> { + Optional + .ofNullable(instance.getCollectedfrom()) + .ifPresent( + cf -> getRelatioPair( + value, relationList, cf, + ModelConstants.IS_PROVIDED_BY, ModelConstants.PROVIDES, hashCodes)); + Optional + .ofNullable(instance.getHostedby()) + .ifPresent( + hb -> getRelatioPair( + value, relationList, hb, + Constants.IS_HOSTED_BY, Constants.HOSTS, hashCodes)); + })); + } + private static void getRelatioPair(R value, List relationList, KeyValue cf, - String result_dtasource, String datasource_result, + String resultDatasource, String datasourceResult, Set hashCodes) { Provenance provenance = Optional .ofNullable(cf.getDataInfo()) @@ -147,7 +152,7 @@ public class Extractor implements Serializable { .map( paction -> Provenance .newInstance( - paction.getClassid(), + paction.getClassname(), dinfo.getTrust())) .orElse( Provenance @@ -162,7 +167,7 @@ public class Extractor implements Serializable { Relation r = getRelation( value.getId(), cf.getKey(), Constants.RESULT_ENTITY, Constants.DATASOURCE_ENTITY, - result_dtasource, ModelConstants.PROVISION, + resultDatasource, ModelConstants.PROVISION, provenance); if (!hashCodes.contains(r.hashCode())) { relationList @@ -173,7 +178,7 @@ public class Extractor implements Serializable { r = getRelation( cf.getKey(), value.getId(), Constants.DATASOURCE_ENTITY, Constants.RESULT_ENTITY, - datasource_result, ModelConstants.PROVISION, + datasourceResult, ModelConstants.PROVISION, provenance); if (!hashCodes.contains(r.hashCode())) { diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java index b0b8b8acd..e1cb0e753 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/Process.java @@ -9,6 +9,7 @@ import org.apache.commons.lang3.StringUtils; import eu.dnetlib.dhp.oa.graph.dump.Constants; import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.MyRuntimeException; import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.Provenance; @@ -43,7 +44,7 @@ public class Process implements Serializable { return (R) ri; } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } @@ -91,7 +92,7 @@ public class Process implements Serializable { return relationList; } catch (final Exception e) { - throw new RuntimeException(e); + throw new MyRuntimeException(e); } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java index 0ed5de67c..fcc4bf39c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystem.java @@ -13,6 +13,8 @@ import org.dom4j.io.SAXReader; import org.jetbrains.annotations.NotNull; import org.xml.sax.SAXException; +import eu.dnetlib.dhp.schema.common.ModelSupport; +import eu.dnetlib.dhp.utils.DHPUtils; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -91,9 +93,9 @@ public class QueryInformationSystem { Element root = doc.getRootElement(); cinfo.setId(root.attributeValue("id")); - Iterator it = root.elementIterator(); + Iterator it = root.elementIterator(); while (it.hasNext()) { - Element el = (Element) it.next(); + Element el = it.next(); if (el.getName().equals("category")) { String categoryId = el.attributeValue("id"); categoryId = categoryId.substring(categoryId.lastIndexOf("::") + 2); @@ -115,14 +117,79 @@ public class QueryInformationSystem { @NotNull private List getCategoryList(Element el, String prefix) { List datasourceList = new ArrayList<>(); - for (Object node : el.selectNodes(".//param")) { - Node n = (Node) node; - if (n.valueOf("./@name").equals("openaireId")) { - datasourceList.add(prefix + "|" + n.getText()); - } + for (Object node : el.selectNodes(".//concept")) { + String oid = getOpenaireId((Node) node, prefix); + if (oid != null) + datasourceList.add(oid); } return datasourceList; } + private String getOpenaireId(Node el, String prefix) { + for (Object node : el.selectNodes(".//param")) { + Node n = (Node) node; + if (n.valueOf("./@name").equals("openaireId")) { + return prefix + "|" + n.getText(); + } + } + + return makeOpenaireId(el, prefix); + + } + + private String makeOpenaireId(Node el, String prefix) { + if (!prefix.equals(ModelSupport.entityIdPrefix.get("project"))) { + return null; + } + String funder = ""; + String grantId = null; + String funding = null; + for (Object node : el.selectNodes(".//param")) { + Node n = (Node) node; + switch (n.valueOf("./@name")) { + case "funding": + funding = n.getText(); + break; + case "funder": + funder = n.getText(); + break; + case "CD_PROJECT_NUMBER": + grantId = n.getText(); + break; + default: + break; + } + } + String nsp = null; + + switch (funder.toLowerCase()) { + case "ec": + if (funding == null) { + return null; + } + if (funding.toLowerCase().contains("h2020")) { + nsp = "corda__h2020::"; + } else { + nsp = "corda_______::"; + } + break; + case "tubitak": + nsp = "tubitakf____::"; + break; + case "dfg": + nsp = "dfgf________::"; + break; + default: + StringBuilder bld = new StringBuilder(); + bld.append(funder.toLowerCase()); + for (int i = funder.length(); i < 12; i++) + bld.append("_"); + bld.append("::"); + nsp = bld.toString(); + } + + return prefix + "|" + nsp + DHPUtils.md5(grantId); + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java index 11c3600dd..ddfd6592f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkDumpRelationJob.java @@ -71,22 +71,22 @@ public class SparkDumpRelationJob implements Serializable { Dataset relations = Utils.readPath(spark, inputPath, Relation.class); relations .map((MapFunction) relation -> { - eu.dnetlib.dhp.schema.dump.oaf.graph.Relation rel_new = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); - rel_new + eu.dnetlib.dhp.schema.dump.oaf.graph.Relation relNew = new eu.dnetlib.dhp.schema.dump.oaf.graph.Relation(); + relNew .setSource( Node .newInstance( relation.getSource(), ModelSupport.idPrefixEntity.get(relation.getSource().substring(0, 2)))); - rel_new + relNew .setTarget( Node .newInstance( relation.getTarget(), ModelSupport.idPrefixEntity.get(relation.getTarget().substring(0, 2)))); - rel_new + relNew .setReltype( RelType .newInstance( @@ -96,26 +96,22 @@ public class SparkDumpRelationJob implements Serializable { Optional odInfo = Optional.ofNullable(relation.getDataInfo()); if (odInfo.isPresent()) { DataInfo dInfo = odInfo.get(); - if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent()) { - if (Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { - rel_new - .setProvenance( - Provenance - .newInstance( - dInfo.getProvenanceaction().getClassname(), - dInfo.getTrust())); - } + if (Optional.ofNullable(dInfo.getProvenanceaction()).isPresent() && + Optional.ofNullable(dInfo.getProvenanceaction().getClassname()).isPresent()) { + relNew + .setProvenance( + Provenance + .newInstance( + dInfo.getProvenanceaction().getClassname(), + dInfo.getTrust())); } } -// Optional -// .ofNullable(relation.getDataInfo()) -// .ifPresent( -// datainfo -> rel_new -// .setProvenance( -// Provenance -// .newInstance(datainfo.getProvenanceaction().getClassname(), datainfo.getTrust()))); + if (Boolean.TRUE.equals(relation.getValidated())) { + relNew.setValidated(relation.getValidated()); + relNew.setValidationDate(relation.getValidationDate()); + } - return rel_new; + return relNew; }, Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Relation.class)) .write() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java index 4365e861f..f9d2123e2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkOrganizationRelation.java @@ -58,7 +58,8 @@ public class SparkOrganizationRelation implements Serializable { final OrganizationMap organizationMap = new Gson() .fromJson(parser.get("organizationCommunityMap"), OrganizationMap.class); - log.info("organization map : {}", new Gson().toJson(organizationMap)); + final String serializedOrganizationMap = new Gson().toJson(organizationMap); + log.info("organization map : {}", serializedOrganizationMap); final String communityMapPath = parser.get("communityMapPath"); log.info("communityMapPath: {}", communityMapPath); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java new file mode 100644 index 000000000..20f3fc4a7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/complete/SparkSelectValidRelationsJob.java @@ -0,0 +1,136 @@ + +package eu.dnetlib.dhp.oa.graph.dump.complete; + +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.Dataset; +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 eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.oa.graph.dump.Utils; +import eu.dnetlib.dhp.schema.oaf.*; + +/** + * It selects the valid relations among those present in the graph. One relation is valid if it is not deletedbyinference + * and if both the source and the target node are present in the graph and are not deleted by inference nor invisible. + * To check this I made a view of the ids of all the entities in the graph, and select the relations for which a join exists + * with this view for both the source and the target + */ + +public class SparkSelectValidRelationsJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkSelectValidRelationsJob.class); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkSelectValidRelationsJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/dump/complete/input_relationdump_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 outputPath = parser.get("outputPath"); + log.info("outputPath: {}", outputPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + Utils.removeOutputDir(spark, outputPath); + selectValidRelation(spark, inputPath, outputPath); + + }); + + } + + private static void selectValidRelation(SparkSession spark, String inputPath, String outputPath) { + Dataset relation = Utils.readPath(spark, inputPath + "/relation", Relation.class); + Dataset publication = Utils.readPath(spark, inputPath + "/publication", Publication.class); + Dataset dataset = Utils + .readPath(spark, inputPath + "/dataset", eu.dnetlib.dhp.schema.oaf.Dataset.class); + Dataset software = Utils.readPath(spark, inputPath + "/software", Software.class); + Dataset other = Utils + .readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class); + Dataset organization = Utils.readPath(spark, inputPath + "/organization", Organization.class); + Dataset project = Utils.readPath(spark, inputPath + "/project", Project.class); + Dataset datasource = Utils.readPath(spark, inputPath + "/datasource", Datasource.class); + + relation.createOrReplaceTempView("relation"); + publication.createOrReplaceTempView("publication"); + dataset.createOrReplaceTempView("dataset"); + other.createOrReplaceTempView("other"); + software.createOrReplaceTempView("software"); + organization.createOrReplaceTempView("organization"); + project.createOrReplaceTempView("project"); + datasource.createOrReplaceTempView("datasource"); + + spark + .sql( + "SELECT id " + + "FROM publication " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM dataset " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM other " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM software " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM organization " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM project " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false " + + "UNION ALL " + + "SELECT id " + + "FROM datasource " + + "WHERE datainfo.deletedbyinference = false AND datainfo.invisible = false ") + .createOrReplaceTempView("identifiers"); + + spark + .sql( + "SELECT relation.* " + + "FROM relation " + + "JOIN identifiers i1 " + + "ON source = i1.id " + + "JOIN identifiers i2 " + + "ON target = i2.id " + + "WHERE datainfo.deletedbyinference = false") + .as(Encoders.bean(Relation.class)) + .write() + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .json(outputPath); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java new file mode 100644 index 000000000..e325c4334 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/MyRuntimeException.java @@ -0,0 +1,30 @@ + +package eu.dnetlib.dhp.oa.graph.dump.exceptions; + +public class MyRuntimeException extends RuntimeException { + + public MyRuntimeException() { + super(); + } + + public MyRuntimeException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public MyRuntimeException(final String message, final Throwable cause) { + super(message, cause); + } + + public MyRuntimeException(final String message) { + super(message); + } + + public MyRuntimeException(final Throwable cause) { + super(cause); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java new file mode 100644 index 000000000..f3fbf740a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/exceptions/NoAvailableEntityTypeException.java @@ -0,0 +1,29 @@ + +package eu.dnetlib.dhp.oa.graph.dump.exceptions; + +public class NoAvailableEntityTypeException extends Exception { + public NoAvailableEntityTypeException() { + super(); + } + + public NoAvailableEntityTypeException( + final String message, + final Throwable cause, + final boolean enableSuppression, + final boolean writableStackTrace) { + super(message, cause, enableSuppression, writableStackTrace); + } + + public NoAvailableEntityTypeException(final String message, final Throwable cause) { + super(message, cause); + } + + public NoAvailableEntityTypeException(final String message) { + super(message); + } + + public NoAvailableEntityTypeException(final Throwable cause) { + super(cause); + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java index d8a1b5c21..6aed9d7a8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkDumpFunderResults.java @@ -17,10 +17,8 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; -import eu.dnetlib.dhp.schema.common.ModelConstants; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.community.Project; -import eu.dnetlib.dhp.schema.oaf.Relation; /** * Splits the dumped results by funder and stores them in a folder named as the funder nsp (for all the funders, but the EC @@ -51,8 +49,8 @@ public class SparkDumpFunderResults implements Serializable { final String outputPath = parser.get("outputPath"); log.info("outputPath: {}", outputPath); - final String relationPath = parser.get("relationPath"); - log.info("relationPath: {}", relationPath); + final String graphPath = parser.get("graphPath"); + log.info("relationPath: {}", graphPath); SparkConf conf = new SparkConf(); @@ -61,18 +59,15 @@ public class SparkDumpFunderResults implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultProjectList(spark, inputPath, outputPath, relationPath); + writeResultProjectList(spark, inputPath, outputPath, graphPath); }); } private static void writeResultProjectList(SparkSession spark, String inputPath, String outputPath, - String relationPath) { + String graphPath) { - Dataset relation = Utils - .readPath(spark, relationPath + "/relation", Relation.class) - .filter( - "dataInfo.deletedbyinference = false and lower(relClass) = '" - + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + Dataset project = Utils + .readPath(spark, graphPath + "/project", eu.dnetlib.dhp.schema.oaf.Project.class); Dataset result = Utils .readPath(spark, inputPath + "/publication", CommunityResult.class) @@ -80,8 +75,8 @@ public class SparkDumpFunderResults implements Serializable { .union(Utils.readPath(spark, inputPath + "/orp", CommunityResult.class)) .union(Utils.readPath(spark, inputPath + "/software", CommunityResult.class)); - List funderList = relation - .select("target") + List funderList = project + .select("id") .map((MapFunction) value -> value.getString(0).substring(0, 15), Encoders.STRING()) .distinct() .collectAsList(); @@ -99,19 +94,26 @@ public class SparkDumpFunderResults implements Serializable { } else { funderdump = fundernsp.substring(0, fundernsp.indexOf("_")).toUpperCase(); } - writeFunderResult(funder, result, outputPath + "/" + funderdump); + writeFunderResult(funder, result, outputPath, funderdump); }); } - private static void writeFunderResult(String funder, Dataset results, String outputPath) { + private static void dumpResults(String nsp, Dataset results, String outputPath, + String funderName) { results.map((MapFunction) r -> { if (!Optional.ofNullable(r.getProjects()).isPresent()) { return null; } for (Project p : r.getProjects()) { - if (p.getId().startsWith(funder)) { + if (p.getId().startsWith(nsp)) { + if (nsp.startsWith("40|irb")) { + if (p.getFunder().getShortName().equals(funderName)) + return r; + else + return null; + } return r; } } @@ -121,7 +123,18 @@ public class SparkDumpFunderResults implements Serializable { .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") - .json(outputPath); + .json(outputPath + "/" + funderName); + } + + private static void writeFunderResult(String funder, Dataset results, String outputPath, + String funderDump) { + + if (funder.startsWith("40|irb")) { + dumpResults(funder, results, outputPath, "HRZZ"); + dumpResults(funder, results, outputPath, "MZOS"); + } else + dumpResults(funder, results, outputPath, funderDump); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java index 2d2b04b5c..d89b9e86d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/dump/funderresults/SparkResultLinkedToProject.java @@ -20,13 +20,13 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.application.ArgumentApplicationParser; import eu.dnetlib.dhp.oa.graph.dump.Utils; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.schema.oaf.Relation; import eu.dnetlib.dhp.schema.oaf.Result; -import scala.Tuple2; /** * Selects the results linked to projects. Only for these results the dump will be performed. - * The code to perform the dump and to expend the dumped results with the informaiton related to projects + * The code to perform the dump and to expend the dumped results with the information related to projects * is the one used for the dump of the community products */ public class SparkResultLinkedToProject implements Serializable { @@ -58,8 +58,8 @@ public class SparkResultLinkedToProject implements Serializable { final String resultClassName = parser.get("resultTableName"); log.info("resultTableName: {}", resultClassName); - final String relationPath = parser.get("relationPath"); - log.info("relationPath: {}", relationPath); + final String graphPath = parser.get("graphPath"); + log.info("graphPath: {}", graphPath); @SuppressWarnings("unchecked") Class inputClazz = (Class) Class.forName(resultClassName); @@ -70,37 +70,47 @@ public class SparkResultLinkedToProject implements Serializable { isSparkSessionManaged, spark -> { Utils.removeOutputDir(spark, outputPath); - writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, relationPath); + writeResultsLinkedToProjects(spark, inputClazz, inputPath, outputPath, graphPath); }); } private static void writeResultsLinkedToProjects(SparkSession spark, Class inputClazz, - String inputPath, String outputPath, String relationPath) { + String inputPath, String outputPath, String graphPath) { Dataset results = Utils .readPath(spark, inputPath, inputClazz) .filter("dataInfo.deletedbyinference = false and datainfo.invisible = false"); Dataset relations = Utils - .readPath(spark, relationPath, Relation.class) + .readPath(spark, graphPath + "/relation", Relation.class) .filter( "dataInfo.deletedbyinference = false and lower(relClass) = '" + ModelConstants.IS_PRODUCED_BY.toLowerCase() + "'"); + Dataset project = Utils.readPath(spark, graphPath + "/project", Project.class); - relations - .joinWith( - results, relations.col("source").equalTo(results.col("id")), - "inner") + results.createOrReplaceTempView("result"); + relations.createOrReplaceTempView("relation"); + project.createOrReplaceTempView("project"); + + Dataset tmp = spark + .sql( + "Select res.* " + + "from relation rel " + + "join result res " + + "on rel.source = res.id " + + "join project p " + + "on rel.target = p.id " + + "") + .as(Encoders.bean(inputClazz)); + tmp .groupByKey( - (MapFunction, String>) value -> value - ._2() + (MapFunction) value -> value .getId(), Encoders.STRING()) - .mapGroups( - (MapGroupsFunction, R>) (k, it) -> it.next()._2(), - Encoders.bean(inputClazz)) + .mapGroups((MapGroupsFunction) (k, it) -> it.next(), Encoders.bean(inputClazz)) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") .json(outputPath); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java index ef419a042..474944260 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java @@ -127,13 +127,6 @@ public class MergeGraphTableSparkJob { } }, Encoders.bean(p_clazz)) .filter((FilterFunction

) Objects::nonNull) - .filter((FilterFunction

) o -> { - HashSet collectedFromNames = Optional - .ofNullable(o.getCollectedfrom()) - .map(c -> c.stream().map(KeyValue::getValue).collect(Collectors.toCollection(HashSet::new))) - .orElse(new HashSet<>()); - return !collectedFromNames.contains("Datacite"); - }) .write() .mode(SaveMode.Overwrite) .option("compression", "gzip") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala new file mode 100644 index 000000000..c7ad1890d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/CopyHdfsOafSparkApplication.scala @@ -0,0 +1,74 @@ +package eu.dnetlib.dhp.oa.graph.raw + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.common.HdfsSupport +import eu.dnetlib.dhp.schema.common.ModelSupport +import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo +import eu.dnetlib.dhp.schema.oaf.Oaf +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.io.IOUtils +import org.apache.commons.lang3.StringUtils +import org.apache.http.client.methods.HttpGet +import org.apache.http.impl.client.HttpClients +import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} +import org.apache.spark.{SparkConf, SparkContext} +import org.slf4j.LoggerFactory + +import scala.collection.JavaConverters._ +import scala.io.Source + +object CopyHdfsOafSparkApplication { + + def main(args: Array[String]): Unit = { + val log = LoggerFactory.getLogger(getClass) + val conf = new SparkConf() + val parser = new ArgumentApplicationParser(Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json")).mkString) + parser.parseArgument(args) + + val spark = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + val sc: SparkContext = spark.sparkContext + + val mdstoreManagerUrl = parser.get("mdstoreManagerUrl") + log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl) + + val mdFormat = parser.get("mdFormat") + log.info("mdFormat: {}", mdFormat) + + val mdLayout = parser.get("mdLayout") + log.info("mdLayout: {}", mdLayout) + + val mdInterpretation = parser.get("mdInterpretation") + log.info("mdInterpretation: {}", mdInterpretation) + + val hdfsPath = parser.get("hdfsPath") + log.info("hdfsPath: {}", hdfsPath) + + implicit val oafEncoder: Encoder[Oaf] = Encoders.kryo[Oaf] + + val paths = DHPUtils.mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation, true).asScala + + val validPaths: List[String] = paths.filter(p => HdfsSupport.exists(p, sc.hadoopConfiguration)).toList + + if (validPaths.nonEmpty) { + val oaf = spark.read.load(validPaths: _*).as[Oaf] + val mapper = new ObjectMapper() + val l =ModelSupport.oafTypes.entrySet.asScala.map(e => e.getKey).toList + l.foreach( + e => + oaf.filter(o => o.getClass.getSimpleName.equalsIgnoreCase(e)) + .map(s => mapper.writeValueAsString(s))(Encoders.STRING) + .write + .option("compression", "gzip") + .mode(SaveMode.Append) + .text(s"$hdfsPath/${e}") + ) + } + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index d78732f9b..e453f7918 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -186,6 +186,9 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i log.info("Processing Openorgs Merge Rels..."); smdbe.execute("queryOpenOrgsSimilarityForProvision.sql", smdbe::processOrgOrgMergeRels); + + log.info("Processing Openorgs Parent/Child Rels..."); + smdbe.execute("queryParentChildRelsOpenOrgs.sql", smdbe::processOrgOrgParentChildRels); break; case openaire_organizations: @@ -689,6 +692,35 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } } + public List processOrgOrgParentChildRels(final ResultSet rs) { + try { + final DataInfo info = prepareDataInfo(rs); // TODO + + final String orgId1 = createOpenaireId(20, rs.getString("source"), true); + final String orgId2 = createOpenaireId(20, rs.getString("target"), true); + + final List collectedFrom = listKeyValues( + createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); + + final Relation r = new Relation(); + r.setRelType(ORG_ORG_RELTYPE); + r.setSubRelType(ModelConstants.RELATIONSHIP); + r + .setRelClass( + rs.getString("type").equalsIgnoreCase("parent") ? ModelConstants.IS_PARENT_OF + : ModelConstants.IS_CHILD_OF); + r.setSource(orgId1); + r.setTarget(orgId2); + r.setCollectedfrom(collectedFrom); + r.setDataInfo(info); + r.setLastupdatetimestamp(lastUpdateTimestamp); + + return Arrays.asList(r); + } catch (final Exception e) { + throw new RuntimeException(e); + } + } + public List processOrgOrgSimRels(final ResultSet rs) { try { final DataInfo info = prepareDataInfo(rs); // TODO diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java index 4110bd806..6c72e4dfc 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java @@ -135,30 +135,4 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication } } - private static Set mdstorePaths(final String mdstoreManagerUrl, - final String format, - final String layout, - final String interpretation) throws IOException { - final String url = mdstoreManagerUrl + "/mdstores/"; - final ObjectMapper objectMapper = new ObjectMapper(); - - final HttpGet req = new HttpGet(url); - - try (final CloseableHttpClient client = HttpClients.createDefault()) { - try (final CloseableHttpResponse response = client.execute(req)) { - final String json = IOUtils.toString(response.getEntity().getContent()); - final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); - return Arrays - .stream(mdstores) - .filter(md -> md.getFormat().equalsIgnoreCase(format)) - .filter(md -> md.getLayout().equalsIgnoreCase(layout)) - .filter(md -> md.getInterpretation().equalsIgnoreCase(interpretation)) - .filter(md -> StringUtils.isNotBlank(md.getHdfsPath())) - .filter(md -> StringUtils.isNotBlank(md.getCurrentVersion())) - .filter(md -> md.getSize() > 0) - .map(md -> md.getHdfsPath() + "/" + md.getCurrentVersion() + "/store") - .collect(Collectors.toSet()); - } - } - } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java index 5d32fe926..cba64899b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/common/AbstractMigrationApplication.java @@ -3,19 +3,30 @@ package eu.dnetlib.dhp.oa.graph.raw.common; import java.io.Closeable; import java.io.IOException; +import java.util.Arrays; +import java.util.Set; import java.util.concurrent.atomic.AtomicInteger; +import java.util.stream.Collectors; +import org.apache.commons.io.IOUtils; +import org.apache.commons.lang3.StringUtils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; import org.apache.hadoop.conf.Configuration; import org.apache.hadoop.fs.Path; import org.apache.hadoop.io.SequenceFile; import org.apache.hadoop.io.Text; +import org.apache.http.client.methods.CloseableHttpResponse; +import org.apache.http.client.methods.HttpGet; +import org.apache.http.impl.client.CloseableHttpClient; +import org.apache.http.impl.client.HttpClients; import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.schema.mdstore.MDStoreWithInfo; import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.utils.DHPUtils; public class AbstractMigrationApplication implements Closeable { @@ -47,6 +58,23 @@ public class AbstractMigrationApplication implements Closeable { SequenceFile.Writer.valueClass(Text.class)); } + /** + * Retrieves from the metadata store manager application the list of paths associated with mdstores characterized + * by he given format, layout, interpretation + * @param mdstoreManagerUrl the URL of the mdstore manager service + * @param format the mdstore format + * @param layout the mdstore layout + * @param interpretation the mdstore interpretation + * @return the set of hdfs paths + * @throws IOException in case of HTTP communication issues + */ + protected static Set mdstorePaths(final String mdstoreManagerUrl, + final String format, + final String layout, + final String interpretation) throws IOException { + return DHPUtils.mdstorePaths(mdstoreManagerUrl, format, layout, interpretation, false); + } + private Configuration getConf() { return new Configuration(); /* diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala new file mode 100644 index 000000000..be217c5c3 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveEntities.scala @@ -0,0 +1,106 @@ +package eu.dnetlib.dhp.oa.graph.resolution + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.common.HdfsSupport +import eu.dnetlib.dhp.schema.common.EntityType +import eu.dnetlib.dhp.schema.oaf.{OtherResearchProduct, Publication, Result, Software, Dataset => OafDataset} +import org.apache.commons.io.IOUtils +import org.apache.hadoop.fs.{FileSystem, Path} +import org.apache.spark.SparkConf +import org.apache.spark.sql._ +import org.slf4j.{Logger, LoggerFactory} + +object SparkResolveEntities { + + val mapper = new ObjectMapper() + val entities = List(EntityType.dataset, EntityType.publication, EntityType.software, EntityType.otherresearchproduct) + + def main(args: Array[String]): Unit = { + val log: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/resolution/resolve_entities_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val graphBasePath = parser.get("graphBasePath") + log.info(s"graphBasePath -> $graphBasePath") + val workingPath = parser.get("workingPath") + log.info(s"workingPath -> $workingPath") + val unresolvedPath = parser.get("unresolvedPath") + log.info(s"unresolvedPath -> $unresolvedPath") + + val targetPath = parser.get("targetPath") + log.info(s"targetPath -> $targetPath") + + + val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration) + fs.mkdirs(new Path(workingPath)) + + resolveEntities(spark, workingPath, unresolvedPath) + generateResolvedEntities(spark, workingPath, graphBasePath, targetPath) + } + + + def resolveEntities(spark: SparkSession, workingPath: String, unresolvedPath: String) = { + implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + import spark.implicits._ + + val rPid: Dataset[(String, String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String, String)] + val up: Dataset[(String, Result)] = spark.read.text(unresolvedPath).as[String].map(s => mapper.readValue(s, classOf[Result])).map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, resEncoder)) + + rPid.joinWith(up, rPid("_2").equalTo(up("_1")), "inner").map { + r => + val result = r._2._2 + val dnetId = r._1._1 + result.setId(dnetId) + result + }.write.mode(SaveMode.Overwrite).save(s"$workingPath/resolvedEntities") + } + + + def deserializeObject(input: String, entity: EntityType): Result = { + + entity match { + case EntityType.publication => mapper.readValue(input, classOf[Publication]) + case EntityType.dataset => mapper.readValue(input, classOf[OafDataset]) + case EntityType.software => mapper.readValue(input, classOf[Software]) + case EntityType.otherresearchproduct => mapper.readValue(input, classOf[OtherResearchProduct]) + } + } + + def generateResolvedEntities(spark: SparkSession, workingPath: String, graphBasePath: String, targetPath:String) = { + + implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + import spark.implicits._ + + val re: Dataset[(String, Result)] = spark.read.load(s"$workingPath/resolvedEntities").as[Result].map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, resEncoder)) + entities.foreach { + e => { + + val currentEntityDataset: Dataset[(String, Result)] = spark.read.text(s"$graphBasePath/$e").as[String].map(s => deserializeObject(s, e)).map(r => (r.getId, r))(Encoders.tuple(Encoders.STRING, resEncoder)) + + currentEntityDataset.joinWith(re, currentEntityDataset("_1").equalTo(re("_1")), "left").map(k => { + + val a = k._1 + val b = k._2 + if (b == null) + a._2 + else { + a._2.mergeFrom(b._2) + a._2 + } + }).map(r => mapper.writeValueAsString(r))(Encoders.STRING) + .write.mode(SaveMode.Overwrite).option("compression", "gzip").text(s"$targetPath/$e") + } + + + } + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala new file mode 100644 index 000000000..a194f2694 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/resolution/SparkResolveRelation.scala @@ -0,0 +1,157 @@ +package eu.dnetlib.dhp.oa.graph.resolution + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.common.HdfsSupport +import eu.dnetlib.dhp.schema.oaf.{Relation, Result} +import eu.dnetlib.dhp.utils.DHPUtils +import org.apache.commons.io.IOUtils +import org.apache.hadoop.fs.{FileSystem, Path} +import org.apache.spark.SparkConf +import org.apache.spark.rdd.RDD +import org.apache.spark.sql._ +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.JsonAST.{JField, JObject, JString} +import org.json4s.jackson.JsonMethods.parse +import org.slf4j.{Logger, LoggerFactory} + +object SparkResolveRelation { + def main(args: Array[String]): Unit = { + val log: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/resolution/resolve_relations_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val graphBasePath = parser.get("graphBasePath") + log.info(s"graphBasePath -> $graphBasePath") + val workingPath = parser.get("workingPath") + log.info(s"workingPath -> $workingPath") + + val targetPath = parser.get("targetPath") + log.info(s"targetPath -> $targetPath") + + implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) + import spark.implicits._ + + + //CLEANING TEMPORARY FOLDER + HdfsSupport.remove(workingPath, spark.sparkContext.hadoopConfiguration) + val fs = FileSystem.get(spark.sparkContext.hadoopConfiguration) + fs.mkdirs(new Path(workingPath)) + + extractPidResolvedTableFromJsonRDD(spark, graphBasePath, workingPath) + + val mapper: ObjectMapper = new ObjectMapper() + + val rPid: Dataset[(String, String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String, String)] + + val relationDs: Dataset[(String, Relation)] = spark.read.text(s"$graphBasePath/relation").as[String] + .map(s => mapper.readValue(s, classOf[Relation])).as[Relation] + .map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) + + relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map { + m => + val sourceResolved = m._2 + val currentRelation = m._1._2 + if (sourceResolved != null && sourceResolved._1 != null && sourceResolved._1.nonEmpty) + currentRelation.setSource(sourceResolved._1) + currentRelation + }.write + .mode(SaveMode.Overwrite) + .save(s"$workingPath/relationResolvedSource") + + + val relationSourceResolved: Dataset[(String, Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation] + .map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) + relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map { + m => + val targetResolved = m._2 + val currentRelation = m._1._2 + if (targetResolved != null && targetResolved._1.nonEmpty) + currentRelation.setTarget(targetResolved._1) + currentRelation + } + .write + .mode(SaveMode.Overwrite) + .save(s"$workingPath/relation_resolved") + + spark.read.load(s"$workingPath/relation_resolved").as[Relation] + .filter(r => !r.getSource.startsWith("unresolved") && !r.getTarget.startsWith("unresolved")) + .map(r => mapper.writeValueAsString(r)) + .write + .option("compression", "gzip") + .mode(SaveMode.Overwrite) + .text(s"$targetPath/relation") + } + + def extractInstanceCF(input: String): List[(String, String)] = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(input) + val result: List[(String, String)] = for { + JObject(iObj) <- json \ "instance" + JField("collectedfrom", JObject(cf)) <- iObj + JField("instancetype", JObject(instancetype)) <- iObj + JField("value", JString(collectedFrom)) <- cf + JField("classname", JString(classname)) <- instancetype + } yield (classname, collectedFrom) + + result + + } + + + def extractPidsFromRecord(input: String): (String, List[(String, String)]) = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(input) + val id: String = (json \ "id").extract[String] + val result: List[(String, String)] = for { + JObject(pids) <- json \\ "instance" \ "pid" + JField("value", JString(pidValue)) <- pids + JField("qualifier", JObject(qualifier)) <- pids + JField("classid", JString(pidType)) <- qualifier + } yield (pidValue, pidType) + + (id, result) + } + + + private def isRelation(input: String): Boolean = { + + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + lazy val json: json4s.JValue = parse(input) + val source = (json \ "source").extractOrElse[String](null) + + source != null + } + + def extractPidResolvedTableFromJsonRDD(spark: SparkSession, graphPath: String, workingPath: String) = { + import spark.implicits._ + + val d: RDD[(String, String)] = spark.sparkContext.textFile(s"$graphPath/*") + .filter(i => !isRelation(i)) + .map(i => extractPidsFromRecord(i)) + .filter(s => s != null && s._1 != null && s._2 != null && s._2.nonEmpty) + .flatMap { p => + p._2.map(pid => + (p._1, DHPUtils.generateUnresolvedIdentifier(pid._1, pid._2)) + ) + }.filter(r => r._1 != null || r._2 != null) + + spark.createDataset(d) + .groupByKey(_._2) + .reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y) + .map(s => s._2) + .write + .mode(SaveMode.Overwrite) + .save(s"$workingPath/relationResolvedPid") + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index cb41d6134..4b82fe645 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -59,7 +59,12 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") - val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation").map(s => mapper.readValue(s, classOf[Relation])) + val relationSemanticFilter = List("cites", "iscitedby","merges", "ismergedin") + + val rddRelation =spark.sparkContext.textFile(s"$sourcePath/relation") + .map(s => mapper.readValue(s, classOf[Relation])) + .filter(r=> r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala index 0a7fc18fb..e4fcd2782 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkCreateScholix.scala @@ -51,10 +51,14 @@ object SparkCreateScholix { relationDS.joinWith(summaryDS, relationDS("_1").equalTo(summaryDS("_1")), "left") .map { input: ((String, Relation), (String, ScholixSummary)) => - val rel: Relation = input._1._2 - val source: ScholixSummary = input._2._2 - (rel.getTarget, ScholixUtils.scholixFromSource(rel, source)) + if (input._1!= null && input._2!= null) { + val rel: Relation = input._1._2 + val source: ScholixSummary = input._2._2 + (rel.getTarget, ScholixUtils.scholixFromSource(rel, source)) + } + else null }(Encoders.tuple(Encoders.STRING, scholixEncoder)) + .filter(r => r!= null) .write.mode(SaveMode.Overwrite).save(s"$targetPath/scholix_from_source") val scholixSource: Dataset[(String, Scholix)] = spark.read.load(s"$targetPath/scholix_from_source").as[(String, Scholix)](Encoders.tuple(Encoders.STRING, scholixEncoder)) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala deleted file mode 100644 index 1b13b81c7..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/SparkResolveRelation.scala +++ /dev/null @@ -1,154 +0,0 @@ -package eu.dnetlib.dhp.sx.graph - -import com.fasterxml.jackson.databind.ObjectMapper -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.schema.oaf.{Relation, Result} -import org.apache.commons.io.IOUtils -import org.apache.hadoop.io.compress.GzipCodec -import org.apache.spark.SparkConf -import org.apache.spark.rdd.RDD -import org.apache.spark.sql._ -import org.json4s -import org.json4s.DefaultFormats -import org.json4s.JsonAST.{JField, JObject, JString} -import org.json4s.jackson.JsonMethods.parse -import org.slf4j.{Logger, LoggerFactory} - -import scala.collection.JavaConverters._ -object SparkResolveRelation { - def main(args: Array[String]): Unit = { - val log: Logger = LoggerFactory.getLogger(getClass) - val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json"))) - parser.parseArgument(args) - val spark: SparkSession = - SparkSession - .builder() - .config(conf) - .appName(getClass.getSimpleName) - .master(parser.get("master")).getOrCreate() - - - val relationPath = parser.get("relationPath") - log.info(s"sourcePath -> $relationPath") - val entityPath = parser.get("entityPath") - log.info(s"entityPath -> $entityPath") - val workingPath = parser.get("workingPath") - log.info(s"workingPath -> $workingPath") - - implicit val relEncoder: Encoder[Relation] = Encoders.kryo(classOf[Relation]) - import spark.implicits._ - - - extractPidResolvedTableFromJsonRDD(spark, entityPath, workingPath) - - val mappper = new ObjectMapper() - - val rPid:Dataset[(String,String)] = spark.read.load(s"$workingPath/relationResolvedPid").as[(String,String)] - - val relationDs:Dataset[(String,Relation)] = spark.read.load(relationPath).as[Relation].map(r => (r.getSource.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) - - relationDs.joinWith(rPid, relationDs("_1").equalTo(rPid("_2")), "left").map{ - m => - val sourceResolved = m._2 - val currentRelation = m._1._2 - if (sourceResolved!=null && sourceResolved._1!=null && sourceResolved._1.nonEmpty) - currentRelation.setSource(sourceResolved._1) - currentRelation - }.write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/relationResolvedSource") - - - val relationSourceResolved:Dataset[(String,Relation)] = spark.read.load(s"$workingPath/relationResolvedSource").as[Relation].map(r => (r.getTarget.toLowerCase, r))(Encoders.tuple(Encoders.STRING, relEncoder)) - relationSourceResolved.joinWith(rPid, relationSourceResolved("_1").equalTo(rPid("_2")), "left").map{ - m => - val targetResolved = m._2 - val currentRelation = m._1._2 - if (targetResolved!=null && targetResolved._1.nonEmpty) - currentRelation.setTarget(targetResolved._1) - currentRelation - }.filter(r => r.getSource.startsWith("50")&& r.getTarget.startsWith("50")) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/relation_resolved") - - spark.read.load(s"$workingPath/relation_resolved").as[Relation] - .map(r => mappper.writeValueAsString(r)) - .rdd.saveAsTextFile(s"$workingPath/relation", classOf[GzipCodec]) - - } - - - def extractPidsFromRecord(input:String):(String,List[(String,String)]) = { - implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - lazy val json: json4s.JValue = parse(input) - val id:String = (json \ "id").extract[String] - val result: List[(String,String)] = for { - JObject(pids) <- json \ "pid" - JField("value", JString(pidValue)) <- pids - JField("qualifier", JObject(qualifier)) <- pids - JField("classname", JString(pidType)) <- qualifier - } yield (pidValue, pidType) - - val alternateIds: List[(String,String)] = for { - JObject(pids) <- json \\ "alternateIdentifier" - JField("value", JString(pidValue)) <- pids - JField("qualifier", JObject(qualifier)) <- pids - JField("classname", JString(pidType)) <- qualifier - } yield (pidValue, pidType) - - (id,result:::alternateIds) - } - - private def extractPidResolvedTableFromJsonRDD(spark: SparkSession, entityPath: String, workingPath: String) = { - import spark.implicits._ - - val d: RDD[(String,String)] = spark.sparkContext.textFile(s"$entityPath/*") - .map(i => extractPidsFromRecord(i)) - .filter(s => s != null && s._1!= null && s._2!=null && s._2.nonEmpty) - .flatMap{ p => - p._2.map(pid => - (p._1, convertPidToDNETIdentifier(pid._1, pid._2)) - ) - }.filter(r =>r._1 != null || r._2 != null) - - spark.createDataset(d) - .groupByKey(_._2) - .reduceGroups((x, y) => if (x._1.startsWith("50|doi") || x._1.startsWith("50|pmid")) x else y) - .map(s => s._2) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/relationResolvedPid") - } - - - /* - This method should be used once we finally convert everythings in Kryo dataset - instead of using rdd of json - */ - private def extractPidResolvedTableFromKryo(spark: SparkSession, entityPath: String, workingPath: String) = { - import spark.implicits._ - implicit val oafEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) - val entities: Dataset[Result] = spark.read.load(s"$entityPath/*").as[Result] - entities.flatMap(e => e.getPid.asScala - .map(p => - convertPidToDNETIdentifier(p.getValue, p.getQualifier.getClassid)) - .filter(s => s != null) - .map(s => (s, e.getId)) - ).groupByKey(_._1) - .reduceGroups((x, y) => if (x._2.startsWith("50|doi") || x._2.startsWith("50|pmid")) x else y) - .map(s => s._2) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/relationResolvedPid") - } - - def convertPidToDNETIdentifier(pid:String, pidType: String):String = { - if (pid==null || pid.isEmpty || pidType== null || pidType.isEmpty) - null - else - s"unresolved::${pid.toLowerCase}::${pidType.toLowerCase}" - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMArticle.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMArticle.java deleted file mode 100644 index 211cbcffb..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMArticle.java +++ /dev/null @@ -1,98 +0,0 @@ - -package eu.dnetlib.dhp.sx.graph.bio.pubmed; - -import java.io.Serializable; -import java.util.ArrayList; -import java.util.List; - -public class PMArticle implements Serializable { - - private String pmid; - private String doi; - private String date; - private PMJournal journal; - private String title; - private String description; - private String language; - private final List subjects = new ArrayList<>(); - private final List publicationTypes = new ArrayList<>(); - private List authors = new ArrayList<>(); - - public List getPublicationTypes() { - return publicationTypes; - } - - private final List grants = new ArrayList<>(); - - public List getGrants() { - return grants; - } - - public String getDoi() { - return doi; - } - - public void setDoi(String doi) { - this.doi = doi; - } - - public String getPmid() { - return pmid; - } - - public void setPmid(String pmid) { - this.pmid = pmid; - } - - public String getDate() { - return date; - } - - public void setDate(String date) { - this.date = date; - } - - public PMJournal getJournal() { - return journal; - } - - public void setJournal(PMJournal journal) { - this.journal = journal; - } - - public String getTitle() { - return title; - } - - public void setTitle(String title) { - this.title = title; - } - - public String getDescription() { - return description; - } - - public void setDescription(String description) { - this.description = description; - } - - public List getAuthors() { - return authors; - } - - public void setAuthors(List authors) { - this.authors = authors; - } - - public List getSubjects() { - return subjects; - } - - public String getLanguage() { - return language; - } - - public void setLanguage(String language) { - this.language = language; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMGrant.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMGrant.java deleted file mode 100644 index 0c3fd4601..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/bio/pubmed/PMGrant.java +++ /dev/null @@ -1,42 +0,0 @@ - -package eu.dnetlib.dhp.sx.graph.bio.pubmed; - -public class PMGrant { - - private String grantID; - private String agency; - private String country; - - public PMGrant() { - } - - public PMGrant(String grantID, String agency, String country) { - this.grantID = grantID; - this.agency = agency; - this.country = country; - } - - public String getGrantID() { - return grantID; - } - - public void setGrantID(String grantID) { - this.grantID = grantID; - } - - public String getAgency() { - return agency; - } - - public void setAgency(String agency) { - this.agency = agency; - } - - public String getCountry() { - return country; - } - - public void setCountry(String country) { - this.country = country; - } -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala index bf726cf59..79c75d6df 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala @@ -1,7 +1,6 @@ package eu.dnetlib.dhp.sx.graph.pangaea import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf import org.apache.spark.rdd.RDD import org.apache.spark.{SparkConf, SparkContext} import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala index 4dafd4fa3..93c554e04 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixUtils.scala @@ -289,7 +289,7 @@ object ScholixUtils { if (r.getInstance() == null || r.getInstance().isEmpty) return List() r.getInstance().asScala.filter(i => i.getUrl!= null && !i.getUrl.isEmpty) - + .filter(i => i.getPid!= null && i.getUrl != null) .flatMap(i => findURLForPID(i.getPid.asScala.toList, i.getUrl.asScala.toList)) .map(i => new ScholixIdentifier(i._1.getValue, i._1.getQualifier.getClassid, i._2)).distinct.toList } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json new file mode 100644 index 000000000..d1b16b09a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/copy_hdfs_oaf_parameters.json @@ -0,0 +1,38 @@ +[ + { + "paramName": "p", + "paramLongName": "hdfsPath", + "paramDescription": "the path where storing the sequential file", + "paramRequired": true + }, + { + "paramName": "u", + "paramLongName": "mdstoreManagerUrl", + "paramDescription": "the MdstoreManager url", + "paramRequired": true + }, + { + "paramName": "f", + "paramLongName": "mdFormat", + "paramDescription": "metadata format", + "paramRequired": true + }, + { + "paramName": "l", + "paramLongName": "mdLayout", + "paramDescription": "metadata layout", + "paramRequired": true + }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "should be yarn or local", + "paramRequired": true + }, + { + "paramName": "i", + "paramLongName": "mdInterpretation", + "paramDescription": "metadata interpretation", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json index 867fd5a77..03cbfb074 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/complete/schema/result_schema.json @@ -1,6 +1,23 @@ { "$schema": "http://json-schema.org/draft-07/schema#", "definitions": { + "AccessRight":{ + "type":"object", + "properties":{ + "code": { + "type": "string", + "description": "COAR access mode code: http://vocabularies.coar-repositories.org/documentation/access_rights/" + }, + "label": { + "type": "string", + "description": "Label for the access mode" + }, + "scheme": { + "type": "string", + "description": "Scheme of reference for access right code. Always set to COAR access rights vocabulary: http://vocabularies.coar-repositories.org/documentation/access_rights/" + } + } + }, "ControlledField": { "type": "object", "properties": { @@ -266,6 +283,57 @@ ] } }, + "instance":{ + "type":"array", + "items":{ + "type":"object", + "properties":{ + "accessright":{ + "allOf":[ + { + "$ref":"#/definitions/AccessRight" + }, + { + "description":"The accessright of this materialization of the result" + } + ] + }, + "articleprocessingcharge":{ + "type":"object", + "properties":{ + "amount":{ + "type":"string" + }, + "currency":{ + "type":"string" + } + } + }, + "license":{ + "type":"string" + }, + "publicationdate":{ + "type":"string" + }, + "refereed":{ + "type":"string" + }, + "type":{ + "type":"string", + "description":"The specific sub-type of this materialization of the result (see https://api.openaire.eu/vocabularies/dnet:result_typologies following the links)" + }, + "url":{ + "description":"Description of url", + "type":"array", + "items":{ + "type":"string", + "description":"urls where it is possible to access the materialization of the result" + } + } + }, + "description":"One of the materialization for this result" + } + }, "programmingLanguage": { "type": "string", "description": "Only for results with type 'software': the programming language" @@ -302,7 +370,7 @@ "subject": { "allOf": [ {"$ref": "#/definitions/ControlledField"}, - {"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary)."}, + {"description": "OpenAIRE subject classification scheme (https://api.openaire.eu/vocabularies/dnet:subject_classification_typologies) and value. When the scheme is 'keyword', it means that the subject is free-text (i.e. not a term from a controlled vocabulary)."} ] } } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json index 9a5a553b1..5dc8e8910 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/funder_result_parameters.json @@ -18,8 +18,8 @@ "paramRequired": false }, { - "paramName": "rp", - "paramLongName": "relationPath", + "paramName": "gp", + "paramLongName": "graphPath", "paramDescription": "the relationPath", "paramRequired": true } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json index 6e42bfa64..677715847 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_cm_parameters.json @@ -18,6 +18,18 @@ "paramLongName": "outputPath", "paramDescription": "the path used to store temporary output files", "paramRequired": true + }, + { + "paramName": "sd", + "paramLongName": "singleDeposition", + "paramDescription": "true if the dump should be created for a single community", + "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "communityId", + "paramDescription": "the id of the community for which to create the dump", + "paramRequired": true } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json index 1d986fc26..e86f6e3d2 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters.json @@ -35,7 +35,12 @@ "paramLongName":"dumpType", "paramDescription": "the type of the dump (complete for the whole graph, community for the products related to communities, funder for the results with at least a link to project", "paramRequired": false - } + }, { + "paramName":"cid", + "paramLongName":"communityId", + "paramDescription": "the id of the community to be dumped", + "paramRequired": false +} ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json index fdd9492fe..f5641bc45 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/input_parameters_link_prj.json @@ -24,8 +24,8 @@ "paramRequired": true }, { - "paramName":"rp", - "paramLongName":"relationPath", + "paramName":"gp", + "paramLongName":"graphPath", "paramDescription": "the path to the relations", "paramRequired": true } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json index 29812188a..dec82bc97 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/split_parameters.json @@ -25,7 +25,12 @@ "paramLongName": "isSparkSessionManaged", "paramDescription": "true if the spark session is managed, false otherwise", "paramRequired": false - } + }, { + "paramName":"cid", + "paramLongName":"communityId", + "paramDescription": "the id of the community to be dumped", + "paramRequired": false +} ] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json index 683b6f4b7..b02062ede 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/upload_zenodo.json @@ -12,12 +12,7 @@ "paramDescription": "The id of the concept record for a new version", "paramRequired": false }, - { - "paramName":"cmp", - "paramLongName":"communityMapPath", - "paramDescription": "the path to the serialization of the community map", - "paramRequired": false - }, + { "paramName":"di", "paramLongName":"depositionId", diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt new file mode 100644 index 000000000..bf55947d1 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/import.txt @@ -0,0 +1,4 @@ +## This is a classpath-based import file (this header is required) +dump_complete classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app +dump_funder classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app +dump_community classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml new file mode 100644 index 000000000..2a612dec5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/main/oozie_app/workflow.xml @@ -0,0 +1,306 @@ + + + + + singleDeposition + Indicates if it is a single community deposition + + + communityId + the id of the community to be dumped if a dump for a single community should be done + + + dumpType + the type of the dump one of {complete, community, funder} + + + onlyUpload + true if the dump is already done and should only be upload in zenodo + + + upload + true if the dump should be upload in zenodo + + + sourcePath + the source path + + + isLookUpUrl + the isLookup service endpoint + + + outputPath + the output path + + + resultAggregation + true if all the result type have to be dumped under result. false otherwise + + + accessToken + the access token used for the deposition in Zenodo + + + connectionUrl + the connection url for Zenodo + + + metadata + the metadata associated to the deposition + + + depositionType + the type of deposition we want to perform. "new" for brand new deposition, "version" for a new version of a published deposition (in this case the concept record id must be provided), "upload" to upload content to an open deposition for which we already have the deposition id (in this case the deposition id should be provided) + + + conceptRecordId + for new version, the id of the record for the old deposition + + + depositionId + the depositionId of a deposition open that has to be added content + + + organizationCommunityMap + the organization community map + + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${wf:conf('onlyUpload') eq true} + + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SaveCommunityMap + --outputPath${workingDir}/communityMap + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + --singleDeposition${singleDeposition} + --communityId${communityId} + + + + + + + + ${wf:conf('dumpType') eq "funder"} + ${wf:conf('dumpType') eq "community"} + + + + + + + + ${wf:appPath()}/dump_complete + + + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + sourcePath + ${sourcePath} + + + organizationCommunityMap + ${organizationCommunityMap} + + + isLookUpUrl + ${isLookUpUrl} + + + resultAggregation + ${resultAggregation} + + + + + + + + + + + ${wf:appPath()}/dump_community + + + + + sourcePath + ${sourcePath} + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + + + + + + + + ${wf:appPath()}/dump_funder + + + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir}/tar + + + sourcePath + ${sourcePath} + + + dumpType + ${dumpType} + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.MakeTar + --hdfsPath${outputPath} + --nameNode${nameNode} + --sourcePath${workingDir}/tar + + + + + + + + ${wf:conf('upload') eq true} + + + + + + + eu.dnetlib.dhp.oa.graph.dump.SendToZenodoHDFS + --hdfsPath${outputPath} + --nameNode${nameNode} + --accessToken${accessToken} + --connectionUrl${connectionUrl} + --metadata${metadata} + --conceptRecordId${conceptRecordId} + --depositionType${depositionType} + --depositionId${depositionId} + + + + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml similarity index 56% rename from dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml index dd3c32c62..e5ec3d0ae 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/datacite/scholix/oozie_app/config-default.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/config-default.xml @@ -12,10 +12,17 @@ true - oozie.action.sharelib.for.spark - spark2 + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire - oozie.launcher.mapreduce.user.classpath.first true diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml new file mode 100644 index 000000000..5f954ff38 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app/workflow.xml @@ -0,0 +1,347 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + communityMapPath + the path to the community map + + + selectedResults + the path the the possible subset ot results to be dumped + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + + + yarn + cluster + Dump table publication for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/dump/publication + --communityMapPath${communityMapPath} + --dumpType${dumpType} + + + + + + + + yarn + cluster + Dump table dataset for community/funder related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/dump/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/dump/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software for community related products + eu.dnetlib.dhp.oa.graph.dump.community.SparkDumpCommunityProducts + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${selectedResults}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/dump/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Prepare association result subset of project info + eu.dnetlib.dhp.oa.graph.dump.community.SparkPrepareResultProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/preparedInfo + + + + + + + + + + + + + + + yarn + cluster + Extend dumped publications with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/publication + --outputPath${outputPath}/ext/publication + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped dataset with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/dataset + --outputPath${outputPath}/ext/dataset + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped ORP with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/otherresearchproduct + --outputPath${outputPath}/ext/orp + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + yarn + cluster + Extend dumped software with information about project + eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/dump/software + --outputPath${outputPath}/ext/software + --preparedInfoPath${workingDir}/preparedInfo + + + + + + + + + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml new file mode 100644 index 000000000..e5ec3d0ae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt new file mode 100644 index 000000000..15387e988 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/import.txt @@ -0,0 +1,2 @@ +## This is a classpath-based import file (this header is required) +dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml new file mode 100644 index 000000000..319517026 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/community/oozie_app/workflow.xml @@ -0,0 +1,145 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + ${wf:appPath()}/dump_common + + + + + sourcePath + ${sourcePath} + + + selectedResults + ${sourcePath} + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir} + + + + + + + + + + + + yarn + cluster + Split dumped result for community + eu.dnetlib.dhp.oa.graph.dump.community.SparkSplitForCommunity + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/ext + --outputPath${outputPath} + --communityMapPath${communityMapPath} + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml new file mode 100644 index 000000000..e5ec3d0ae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml new file mode 100644 index 000000000..f84ab7e1a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/complete/oozie_app/workflow.xml @@ -0,0 +1,537 @@ + + + + sourcePath + the source path + + + outputPath + the output path + + + resultAggregation + true if all the result type have to be dumped under result. false otherwise + + + organizationCommunityMap + the organization community map + + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + + + + + + + + + + + + + + + yarn + cluster + Dump table publication + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table dataset + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/result/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/result/otherresearchproduct + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/result/software + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table organization + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/organization + --resultTableNameeu.dnetlib.dhp.schema.oaf.Organization + --outputPath${outputPath}/organization + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table project + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/project + --resultTableNameeu.dnetlib.dhp.schema.oaf.Project + --outputPath${outputPath}/project + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table datasource + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpEntitiesJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/datasource + --resultTableNameeu.dnetlib.dhp.schema.oaf.Datasource + --outputPath${outputPath}/datasource + --communityMapPath${workingDir}/communityMap + + + + + + + + yarn + cluster + Select valid table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkSelectValidRelationsJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath} + --outputPath${workingDir}/validrelation + + + + + + + + yarn + cluster + Dump table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkDumpRelationJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/validrelation + --outputPath${workingDir}/relation/relation + + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextEntities + --hdfsPath${outputPath}/communities_infrastructures/communities_infrastructure.json.gz + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + eu.dnetlib.dhp.oa.graph.dump.complete.CreateContextRelation + --hdfsPath${workingDir}/relation/context + --nameNode${nameNode} + --isLookUpUrl${isLookUpUrl} + + + + + + + + yarn + cluster + Dump table relation + eu.dnetlib.dhp.oa.graph.dump.complete.SparkOrganizationRelation + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/relation + --outputPath${workingDir}/relation/contextOrg + --organizationCommunityMap${organizationCommunityMap} + --communityMapPath${communityMapPath} + + + + + + + + + + + + + + + + + yarn + cluster + Extract Relations from publication + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/relation/publication + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table dataset + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/relation/dataset + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table ORP + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/relation/orp + --communityMapPath${communityMapPath} + + + + + + + + yarn + cluster + Dump table software + eu.dnetlib.dhp.oa.graph.dump.complete.SparkExtractRelationFromEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/relation/software + --communityMapPath${communityMapPath} + + + + + + + + + + yarn + cluster + Collect Results and Relations and put them in the right path + eu.dnetlib.dhp.oa.graph.dump.complete.SparkCollectAndSave + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir} + --outputPath${outputPath} + --resultAggregation${resultAggregation} + + + + + + + + + Sub-workflow dump complete failed with error message ${wf:errorMessage()} + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml new file mode 100644 index 000000000..e5ec3d0ae --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt new file mode 100644 index 000000000..15387e988 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/import.txt @@ -0,0 +1,2 @@ +## This is a classpath-based import file (this header is required) +dump_common classpath eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/commoncommunityfunder/oozie_app \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml new file mode 100644 index 000000000..b990f4e49 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/dump/wf/subworkflows/funder/oozie_app/workflow.xml @@ -0,0 +1,256 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + hiveDbName + the target hive database name + + + hiveJdbcUrl + hive server jdbc url + + + hiveMetastoreUris + hive server metastore URIs + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/publication + --resultTableNameeu.dnetlib.dhp.schema.oaf.Publication + --outputPath${workingDir}/result/publication + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/dataset + --resultTableNameeu.dnetlib.dhp.schema.oaf.Dataset + --outputPath${workingDir}/result/dataset + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/otherresearchproduct + --resultTableNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --outputPath${workingDir}/result/otherresearchproduct + --graphPath${sourcePath} + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkResultLinkedToProject + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${sourcePath}/software + --resultTableNameeu.dnetlib.dhp.schema.oaf.Software + --outputPath${workingDir}/result/software + --graphPath${sourcePath} + + + + + + + + + + ${wf:appPath()}/dump_common + + + + + sourcePath + ${sourcePath} + + + selectedResults + ${workingDir}/result + + + communityMapPath + ${workingDir}/communityMap + + + outputPath + ${workingDir} + + + + + + + + + + yarn + cluster + Dump funder results + eu.dnetlib.dhp.oa.graph.dump.funderresults.SparkDumpFunderResults + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --sourcePath${workingDir}/ext + --outputPath${outputPath} + --graphPath${sourcePath} + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml index 321ca4090..307e26267 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_all/oozie_app/workflow.xml @@ -258,7 +258,7 @@ ${wf:conf('reuseDB') eq false} ${wf:conf('reuseDB') eq true} - + @@ -544,6 +544,33 @@ --sourcePath${workingDir}/entities --graphRawPath${workingDir}/graph_raw + + + + + + + yarn + cluster + ImportOAF_hdfs_graph + eu.dnetlib.dhp.oa.graph.raw.CopyHdfsOafSparkApplication + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory ${sparkExecutorMemory} + --executor-cores ${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --hdfsPath${workingDir}/graph_raw + --mdstoreManagerUrl${mdstoreManagerUrl} + --mdFormatOAF + --mdLayoutstore + --masteryarn + --mdInterpretationgraph + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/config-default.xml similarity index 100% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/config-default.xml rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/config-default.xml diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml new file mode 100644 index 000000000..3cd08bc9b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/oozie_app/workflow.xml @@ -0,0 +1,170 @@ + + + + graphBasePath + the path of the graph + + + unresolvedPath + the path of the unresolved Entities + + + targetPath + the target path after resolution + + + shouldResolveEntities + true + allows to activate/deactivate the resolution process over the entities + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + yarn + cluster + Resolve Relations in raw graph + eu.dnetlib.dhp.oa.graph.resolution.SparkResolveRelation + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=15000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --graphBasePath${graphBasePath} + --workingPath${workingDir} + --targetPath${targetPath} + + + + + + + + ${wf:conf('shouldResolveEntities') eq false} + ${wf:conf('shouldResolveEntities') eq true} + + + + + + + yarn + cluster + Resolve Entities in raw graph + eu.dnetlib.dhp.oa.graph.resolution.SparkResolveEntities + dhp-graph-mapper-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.shuffle.partitions=10000 + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + + --masteryarn + --graphBasePath${graphBasePath} + --unresolvedPath${unresolvedPath} + --workingPath${workingDir} + --targetPath${targetPath} + + + + + + + + + + + + + + + ${nameNode}/${graphBasePath}/publication + ${nameNode}/${targetPath}/publication + + + + + + + + ${nameNode}/${graphBasePath}/dataset + ${nameNode}/${targetPath}/dataset + + + + + + + + ${nameNode}/${graphBasePath}/otherresearchproduct + ${nameNode}/${targetPath}/otherresearchproduct + + + + + + + + ${nameNode}/${graphBasePath}/software + ${nameNode}/${targetPath}/software + + + + + + + + + + + + + + + + ${nameNode}/${graphBasePath}/organization + ${nameNode}/${targetPath}/organization + + + + + + + + ${nameNode}/${graphBasePath}/project + ${nameNode}/${targetPath}/project + + + + + + + + ${nameNode}/${graphBasePath}/datasource + ${nameNode}/${targetPath}/datasource + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_entities_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_entities_params.json new file mode 100644 index 000000000..67e315664 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_entities_params.json @@ -0,0 +1,7 @@ +[ + {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, + {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true}, + {"paramName":"u", "paramLongName":"unresolvedPath", "paramDescription": "the source Path", "paramRequired": true}, + {"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target path", "paramRequired": true} +] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_relations_params.json similarity index 50% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_relations_params.json index f211adb9a..66a035da5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolve_relations_params.json +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/resolution/resolve_relations_params.json @@ -1,6 +1,6 @@ [ {"paramName":"mt", "paramLongName":"master", "paramDescription": "should be local or yarn", "paramRequired": true}, - {"paramName":"r", "paramLongName":"relationPath", "paramDescription": "the source Path", "paramRequired": true}, {"paramName":"w", "paramLongName":"workingPath", "paramDescription": "the source Path", "paramRequired": true}, - {"paramName":"e", "paramLongName":"entityPath", "paramDescription": "the path of the raw graph", "paramRequired": true} + {"paramName":"g", "paramLongName":"graphBasePath", "paramDescription": "the path of the raw graph", "paramRequired": true}, + {"paramName":"t", "paramLongName":"targetPath", "paramDescription": "the target path", "paramRequired": true} ] \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql new file mode 100644 index 000000000..388fee3f5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryParentChildRelsOpenOrgs.sql @@ -0,0 +1,13 @@ +SELECT + id1 AS source, + id2 AS target, + reltype AS type, + false AS inferred, + false AS deletedbyinference, + 0.95 AS trust, + '' AS inferenceprovenance, + 'openaire____::openorgs' AS collectedfromid, + 'OpenOrgs Database' AS collectedfromname, + 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction +FROM relationships +WHERE reltype = 'Child' OR reltype = 'Parent' \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/workflow.xml deleted file mode 100644 index 0df085ee1..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/bio/oozie_app/workflow.xml +++ /dev/null @@ -1,177 +0,0 @@ - - - - PDBPath - the PDB Database Working Path - - - - UNIPROTDBPath - the UNIPROT Database Working Path - - - - EBIDataset - the EBI Links Dataset Path - - - - ScholixResolvedDBPath - the Scholix Resolved Dataset Path - - - - CrossrefLinksPath - the CrossrefLinks Path - - - targetPath - the Target Working dir path - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - yarn - cluster - Convert PDB to OAF Dataset - eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --dbPath${PDBPath} - --databasePDB - --targetPath${targetPath}/pdb_OAF - - - - - - - - - yarn - cluster - Convert UNIPROT to OAF Dataset - eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --dbPath${UNIPROTDBPath} - --databaseUNIPROT - --targetPath${targetPath}/uniprot_OAF - - - - - - - - - yarn - cluster - Convert EBI Links to OAF Dataset - eu.dnetlib.dhp.sx.graph.ebi.SparkEBILinksToOaf - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --sourcePath${EBIDataset} - --targetPath${targetPath}/ebi_OAF - - - - - - - - - yarn - cluster - Convert Scholix to OAF Dataset - eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --dbPath${ScholixResolvedDBPath} - --databaseSCHOLIX - --targetPath${targetPath}/scholix_resolved_OAF - - - - - - - - - yarn - cluster - Convert Crossref Links to OAF Dataset - eu.dnetlib.dhp.sx.graph.bio.SparkTransformBioDatabaseToOAF - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --dbPath${CrossrefLinksPath} - --databaseCROSSREF_LINKS - --targetPath${targetPath}/crossref_unresolved_relation_OAF - - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml deleted file mode 100644 index 7612321c0..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/oozie_app/workflow.xml +++ /dev/null @@ -1,99 +0,0 @@ - - - - workingPath - the Working Path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - yarn-cluster - cluster - Create Baselnie DataSet - - eu.dnetlib.dhp.sx.ebi.SparkCreateBaselineDataFrame - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=1 - --driver-memory=${sparkDriverMemory} - --executor-cores=${sparkExecutorCores} - ${sparkExtraOPT} - - --workingPath${workingPath} - --masteryarn - --hdfsServerUri${nameNode} - - - - - - - - yarn-cluster - cluster - Create EBI DataSet - - eu.dnetlib.dhp.sx.ebi.SparkEBILinksToOaf - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.sql.shuffle.partitions=1000 - ${sparkExtraOPT} - - --workingPath${workingPath} - --masteryarn - - - - - - - - yarn-cluster - cluster - Create Baseline DataSet - - eu.dnetlib.dhp.sx.ebi.SparkAddLinkUpdates - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=1 - --driver-memory=${sparkDriverMemory} - --executor-cores=${sparkExecutorCores} - ${sparkExtraOPT} - - --workingPath${workingPath} - --masteryarn - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml deleted file mode 100644 index cd3bb8c71..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/ebi/update/oozie_app/workflow.xml +++ /dev/null @@ -1,67 +0,0 @@ - - - - sourcePath - the Working Path - - - workingPath - the Working Path - - - sparkDriverMemory - memory for driver process - - - sparkExecutorMemory - memory for individual executor - - - sparkExecutorCores - number of cores used by single executor - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - yarn-cluster - cluster - Incremental Download EBI Links - eu.dnetlib.dhp.sx.graph.ebi.SparkDownloadEBILinks - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=2000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --sourcePath${sourcePath} - --workingPath${workingPath} - --masteryarn - - - - - - - - - - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml index d8eb1fc80..17996c82c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/finalGraph/oozie_app/workflow.xml @@ -54,7 +54,7 @@ --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=5000 + --conf spark.sql.shuffle.partitions=20000 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} @@ -79,7 +79,7 @@ --executor-cores=${sparkExecutorCores} --driver-memory=${sparkDriverMemory} --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=6000 + --conf spark.sql.shuffle.partitions=20000 --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml deleted file mode 100644 index 7683ff94c..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/sx/graph/resolverelation/oozie_app/workflow.xml +++ /dev/null @@ -1,62 +0,0 @@ - - - - entityPath - the path of deduplicate Entities - - - relationPath - the path of relation unresolved - - - targetPath - the path of relation unresolved - - - - - - - - Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - - - - - - - - - - - - - - - yarn - cluster - Resolve Relations in raw graph - eu.dnetlib.dhp.sx.graph.SparkResolveRelation - dhp-graph-mapper-${projectVersion}.jar - - --executor-memory=${sparkExecutorMemory} - --executor-cores=${sparkExecutorCores} - --driver-memory=${sparkDriverMemory} - --conf spark.extraListeners=${spark2ExtraListeners} - --conf spark.sql.shuffle.partitions=3000 - --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} - --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} - --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} - - --masteryarn - --relationPath${relationPath} - --workingPath${targetPath} - --entityPath${entityPath} - - - - - - \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java index 42d9f226c..c8a368dd6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java @@ -8,9 +8,12 @@ import java.io.IOException; import java.util.Collection; import java.util.List; import java.util.Set; +import java.util.stream.Collectors; import java.util.stream.Stream; import org.apache.commons.io.IOUtils; +import org.apache.hadoop.hdfs.server.datanode.fsdataset.impl.MappableBlock; +import org.junit.jupiter.api.Assertions; import org.junit.jupiter.api.BeforeEach; import org.junit.jupiter.api.Test; import org.junit.jupiter.api.extension.ExtendWith; @@ -137,9 +140,21 @@ public class GraphCleaningFunctionsTest { .stream() .anyMatch(s -> s.getValue().equals("10.1009/qwerty"))); + assertEquals(5, p_out.getTitle().size()); + Publication p_cleaned = GraphCleaningFunctions.cleanup(p_out); - assertEquals(1, p_cleaned.getTitle().size()); + assertEquals(3, p_cleaned.getTitle().size()); + + List titles = p_cleaned + .getTitle() + .stream() + .map(StructuredProperty::getValue) + .collect(Collectors.toList()); + assertTrue(titles.contains("omic")); + assertTrue( + titles.contains("Optical response of strained- and unstrained-silicon cold-electron bolometers test")); + assertTrue(titles.contains("｢マキャベリ的知性と心の理論の進化論｣ リチャード・バーン， アンドリュー・ホワイトゥン 編／藤田和生， 山下博志， 友永雅巳 監訳")); assertEquals("CLOSED", p_cleaned.getBestaccessright().getClassid()); assertNull(p_out.getPublisher()); @@ -209,4 +224,27 @@ public class GraphCleaningFunctionsTest { .readLines( GraphCleaningFunctionsTest.class.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/synonyms.txt")); } + + @Test + public void testCleanDoiBoost() throws IOException { + String json = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping); + Publication cleaned = GraphCleaningFunctions.cleanup(p_out); + + Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned)); + } + + @Test + public void testCleanDoiBoost2() throws IOException { + String json = IOUtils + .toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/doiboostpub2.json")); + Publication p_in = MAPPER.readValue(json, Publication.class); + Publication p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping); + Publication cleaned = GraphCleaningFunctions.cleanup(p_out); + + Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned)); + + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java index 7c69c9635..602aaf6e6 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/DumpJobTest.java @@ -11,17 +11,21 @@ import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; -import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; import org.junit.jupiter.api.*; import org.slf4j.Logger; import org.slf4j.LoggerFactory; +import com.fasterxml.jackson.core.JsonProcessingException; import com.fasterxml.jackson.databind.ObjectMapper; import com.google.gson.Gson; import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; import eu.dnetlib.dhp.schema.oaf.Dataset; @@ -137,6 +141,511 @@ public class DumpJobTest { System.out.println(new Gson().toJson(map)); } + @Test + public void testPublicationDump() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getMeasures().size()); + Assertions + .assertTrue( + gr + .getMeasures() + .stream() + .anyMatch( + m -> m.getKey().equals("influence") + && m.getValue().equals("1.62759106106e-08"))); + Assertions + .assertTrue( + gr + .getMeasures() + .stream() + .anyMatch( + m -> m.getKey().equals("popularity") + && m.getValue().equals("0.22519296"))); + + Assertions.assertEquals(6, gr.getAuthor().size()); + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Nikolaidou,Charitini") && + a.getName().equals("Charitini") && a.getSurname().equals("Nikolaidou") + && a.getRank() == 1 && a.getPid() == null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Votsi,Nefta") && + a.getName().equals("Nefta") && a.getSurname().equals("Votsi") + && a.getRank() == 2 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Sgardelis,Steanos") && + a.getName().equals("Steanos") && a.getSurname().equals("Sgardelis") + && a.getRank() == 3 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Halley,John") && + a.getName().equals("John") && a.getSurname().equals("Halley") + && a.getRank() == 4 && a.getPid() == null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Pantis,John") && + a.getName().equals("John") && a.getSurname().equals("Pantis") + && a.getRank() == 5 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); + + Assertions + .assertTrue( + gr + .getAuthor() + .stream() + .anyMatch( + a -> a.getFullname().equals("Tsiafouli,Maria") && + a.getName().equals("Maria") && a.getSurname().equals("Tsiafouli") + && a.getRank() == 6 && a.getPid().getId().getScheme().equals(ModelConstants.ORCID_PENDING) + && a.getPid().getId().getValue().equals("0000-0001-6651-1178") + && a.getPid().getProvenance() != null)); + + Assertions.assertEquals("publication", gr.getType()); + + Assertions.assertEquals("eng", gr.getLanguage().getCode()); + Assertions.assertEquals("English", gr.getLanguage().getLabel()); + + Assertions.assertEquals(1, gr.getCountry().size()); + Assertions.assertEquals("IT", gr.getCountry().get(0).getCode()); + Assertions.assertEquals("Italy", gr.getCountry().get(0).getLabel()); + Assertions.assertTrue(gr.getCountry().get(0).getProvenance() == null); + + Assertions.assertEquals(12, gr.getSubjects().size()); + Assertions + .assertTrue( + gr + .getSubjects() + .stream() + .anyMatch( + s -> s.getSubject().getValue().equals("Ecosystem Services hotspots") + && s.getSubject().getScheme().equals("ACM") && s.getProvenance() != null && + s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); + Assertions + .assertTrue( + gr + .getSubjects() + .stream() + .anyMatch( + s -> s.getSubject().getValue().equals("Natura 2000") + && s.getSubject().getScheme().equals("") && s.getProvenance() != null && + s.getProvenance().getProvenance().equals("sysimport:crosswalk:repository"))); + + Assertions + .assertEquals( + "Ecosystem Service capacity is higher in areas of multiple designation types", + gr.getMaintitle()); + + Assertions.assertEquals(null, gr.getSubtitle()); + + Assertions.assertEquals(1, gr.getDescription().size()); + + Assertions + .assertTrue( + gr + .getDescription() + .get(0) + .startsWith("The implementation of the Ecosystem Service (ES) concept into practice")); + Assertions + .assertTrue( + gr + .getDescription() + .get(0) + .endsWith( + "start complying with new standards and demands for nature conservation and environmental management.")); + + Assertions.assertEquals("2017-01-01", gr.getPublicationdate()); + + Assertions.assertEquals("Pensoft Publishers", gr.getPublisher()); + + Assertions.assertEquals(null, gr.getEmbargoenddate()); + + Assertions.assertEquals(1, gr.getSource().size()); + Assertions.assertEquals("One Ecosystem 2: e13718", gr.getSource().get(0)); + + Assertions.assertEquals(1, gr.getFormat().size()); + Assertions.assertEquals("text/html", gr.getFormat().get(0)); + + Assertions.assertEquals(0, gr.getContributor().size()); + + Assertions.assertEquals(0, gr.getCoverage().size()); + + Assertions.assertEquals(ModelConstants.ACCESS_RIGHT_OPEN, gr.getBestaccessright().getLabel()); + Assertions + .assertEquals( + Constants.accessRightsCoarMap.get(ModelConstants.ACCESS_RIGHT_OPEN), gr.getBestaccessright().getCode()); + + Assertions.assertEquals("One Ecosystem", gr.getContainer().getName()); + Assertions.assertEquals("2367-8194", gr.getContainer().getIssnOnline()); + Assertions.assertEquals("", gr.getContainer().getIssnPrinted()); + Assertions.assertEquals("", gr.getContainer().getIssnLinking()); + + Assertions.assertTrue(null == gr.getDocumentationUrl() || gr.getDocumentationUrl().size() == 0); + + Assertions.assertTrue(null == gr.getCodeRepositoryUrl()); + + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + + Assertions.assertTrue(null == gr.getContactperson() || gr.getContactperson().size() == 0); + + Assertions.assertTrue(null == gr.getContactgroup() || gr.getContactgroup().size() == 0); + + Assertions.assertTrue(null == gr.getTool() || gr.getTool().size() == 0); + + Assertions.assertEquals(null, gr.getSize()); + + Assertions.assertEquals(null, gr.getVersion()); + + Assertions.assertTrue(null == gr.getGeolocation() || gr.getGeolocation().size() == 0); + + Assertions.assertEquals("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2", gr.getId()); + + Assertions.assertEquals(2, gr.getOriginalId().size()); + Assertions + .assertTrue( + gr.getOriginalId().contains("50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2") + && gr.getOriginalId().contains("10.3897/oneeco.2.e13718")); + + Assertions.assertEquals(1, gr.getPid().size()); + Assertions + .assertTrue( + gr.getPid().get(0).getScheme().equals("doi") + && gr.getPid().get(0).getValue().equals("10.1016/j.triboint.2014.05.004")); + + Assertions.assertEquals("2020-03-23T00:20:51.392Z", gr.getDateofcollection()); + + Assertions.assertEquals(1, gr.getInstance().size()); + + Instance instance = gr.getInstance().get(0); + Assertions.assertEquals(0, instance.getPid().size()); + Assertions.assertEquals(1, instance.getAlternateIdentifier().size()); + Assertions + .assertTrue( + instance.getAlternateIdentifier().get(0).getScheme().equals("doi") + && instance.getAlternateIdentifier().get(0).getValue().equals("10.3897/oneeco.2.e13718")); + Assertions.assertEquals(null, instance.getLicense()); + Assertions + .assertTrue( + instance + .getAccessright() + .getCode() + .equals( + Constants.accessRightsCoarMap + .get(ModelConstants.ACCESS_RIGHT_OPEN))); + Assertions.assertTrue(instance.getAccessright().getLabel().equals(ModelConstants.ACCESS_RIGHT_OPEN)); + Assertions.assertTrue(instance.getAccessright().getOpenAccessRoute().equals(OpenAccessRoute.green)); + Assertions.assertTrue(instance.getType().equals("Article")); + Assertions.assertEquals(2, instance.getUrl().size()); + Assertions + .assertTrue( + instance.getUrl().contains("https://doi.org/10.3897/oneeco.2.e13718") + && instance.getUrl().contains("https://oneecosystem.pensoft.net/article/13718/")); + Assertions.assertEquals("2017-01-01", instance.getPublicationdate()); + Assertions.assertEquals(null, instance.getArticleprocessingcharge()); + Assertions.assertEquals("peerReviewed", instance.getRefereed()); + } + + @Test + public void testDatasetDump() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/dataset_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, Dataset.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'dataset'").count()); + + // the common fields in the result have been already checked. Now checking only + // community specific fields + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getGeolocation().size()); + Assertions.assertEquals(2, gr.getGeolocation().stream().filter(gl -> gl.getBox().equals("")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPlace().equals("")).count()); + Assertions.assertEquals(1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("")).count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> gl.getPlace().equals("18 York St, Ottawa, ON K1N 5S6; Ottawa; Ontario; Canada")) + .count()); + Assertions + .assertEquals( + 1, gr.getGeolocation().stream().filter(gl -> gl.getPoint().equals("45.427242 -75.693904")).count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> gl.getPoint().equals("") && !gl.getPlace().equals("")) + .count()); + Assertions + .assertEquals( + 1, + gr + .getGeolocation() + .stream() + .filter(gl -> !gl.getPoint().equals("") && gl.getPlace().equals("")) + .count()); + + Assertions.assertEquals("1024Gb", gr.getSize()); + + Assertions.assertEquals("1.01", gr.getVersion()); + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + Assertions.assertEquals(null, gr.getDocumentationUrl()); + Assertions.assertEquals(null, gr.getContactperson()); + Assertions.assertEquals(null, gr.getContactgroup()); + Assertions.assertEquals(null, gr.getTool()); + + } + + @Test + public void testSoftwareDump() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/software_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, Software.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'software'").count()); + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getDocumentationUrl().size()); + Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_1")); + Assertions.assertTrue(gr.getDocumentationUrl().contains("doc_url_2")); + + Assertions.assertEquals("code_repo", gr.getCodeRepositoryUrl()); + + Assertions.assertEquals("perl", gr.getProgrammingLanguage()); + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getContactperson()); + Assertions.assertEquals(null, gr.getContactgroup()); + Assertions.assertEquals(null, gr.getTool()); + Assertions.assertEquals(null, gr.getGeolocation()); + Assertions.assertEquals(null, gr.getSize()); + Assertions.assertEquals(null, gr.getVersion()); + + } + + @Test + public void testOrpDump() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/orp_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", + communityMapPath, OtherResearchProduct.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'other'").count()); + + GraphResult gr = verificationDataset.first(); + + Assertions.assertEquals(2, gr.getContactperson().size()); + Assertions.assertTrue(gr.getContactperson().contains(("contact_person1"))); + Assertions.assertTrue(gr.getContactperson().contains(("contact_person2"))); + + Assertions.assertEquals(1, gr.getContactgroup().size()); + Assertions.assertTrue(gr.getContactgroup().contains(("contact_group"))); + + Assertions.assertEquals(2, gr.getTool().size()); + Assertions.assertTrue(gr.getTool().contains("tool1")); + Assertions.assertTrue(gr.getTool().contains("tool2")); + + Assertions.assertEquals(null, gr.getContainer()); + Assertions.assertEquals(null, gr.getDocumentationUrl()); + Assertions.assertEquals(null, gr.getCodeRepositoryUrl()); + Assertions.assertEquals(null, gr.getProgrammingLanguage()); + Assertions.assertEquals(null, gr.getGeolocation()); + Assertions.assertEquals(null, gr.getSize()); + Assertions.assertEquals(null, gr.getVersion()); + + } + + @Test + public void testPublicationDumpCommunity() throws JsonProcessingException { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_extendedinstance") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + Assertions.assertEquals(1, verificationDataset.count()); + + Assertions.assertEquals(1, verificationDataset.filter("type = 'publication'").count()); + + // the common fields in the result have been already checked. Now checking only + // community specific fields + + CommunityResult cr = verificationDataset.first(); + + Assertions.assertEquals(1, cr.getContext().size()); + Assertions.assertEquals("dh-ch", cr.getContext().get(0).getCode()); + Assertions.assertEquals("Digital Humanities and Cultural Heritage", cr.getContext().get(0).getLabel()); + Assertions.assertEquals(1, cr.getContext().get(0).getProvenance().size()); + Assertions.assertEquals("Inferred by OpenAIRE", cr.getContext().get(0).getProvenance().get(0).getProvenance()); + Assertions.assertEquals("0.9", cr.getContext().get(0).getProvenance().get(0).getTrust()); + + Assertions.assertEquals(1, cr.getCollectedfrom().size()); + Assertions + .assertEquals("10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", cr.getCollectedfrom().get(0).getKey()); + Assertions.assertEquals("Pensoft", cr.getCollectedfrom().get(0).getValue()); + + Assertions.assertEquals(1, cr.getInstance().size()); + Assertions + .assertEquals( + "10|openaire____::fdc7e0400d8c1634cdaf8051dbae23db", + cr.getInstance().get(0).getCollectedfrom().getKey()); + Assertions.assertEquals("Pensoft", cr.getInstance().get(0).getCollectedfrom().getValue()); + Assertions + .assertEquals( + "10|openaire____::e707e544b9a5bd23fc27fbfa65eb60dd", cr.getInstance().get(0).getHostedby().getKey()); + Assertions.assertEquals("One Ecosystem", cr.getInstance().get(0).getHostedby().getValue()); + + } + @Test public void testDataset() { @@ -151,7 +660,6 @@ public class DumpJobTest { DumpProducts dump = new DumpProducts(); dump .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); @@ -166,10 +674,6 @@ public class DumpJobTest { Assertions.assertEquals(90, verificationDataset.count()); -// verificationDataset -// .filter("id = '50|DansKnawCris::1a960e20087cb46b93588e4e184e8a58'") -// .foreach((ForeachFunction) rec -> System.out.println(OBJECT_MAPPER.writeValueAsString(rec))); - Assertions .assertTrue( verificationDataset.filter("bestAccessright.code = 'c_abf2'").count() == verificationDataset @@ -198,8 +702,6 @@ public class DumpJobTest { Assertions.assertTrue(verificationDataset.filter("type = 'dataset'").count() == 90); -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) - } @Test @@ -231,8 +733,6 @@ public class DumpJobTest { Assertions.assertEquals(5, verificationDataset.count()); - verificationDataset - .foreach((ForeachFunction) res -> System.out.println(OBJECT_MAPPER.writeValueAsString(res))); } @Test @@ -249,7 +749,6 @@ public class DumpJobTest { DumpProducts dump = new DumpProducts(); dump .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Dataset.class, CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); @@ -264,7 +763,6 @@ public class DumpJobTest { Assertions.assertEquals(0, verificationDataset.count()); - verificationDataset.show(false); } @Test @@ -299,8 +797,6 @@ public class DumpJobTest { Assertions.assertEquals(74, verificationDataset.filter("type = 'publication'").count()); -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) - } @Test @@ -333,9 +829,6 @@ public class DumpJobTest { Assertions.assertEquals(6, verificationDataset.count()); Assertions.assertEquals(6, verificationDataset.filter("type = 'software'").count()); - verificationDataset.show(false); - -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) } @@ -369,9 +862,6 @@ public class DumpJobTest { Assertions.assertEquals(3, verificationDataset.count()); Assertions.assertEquals(3, verificationDataset.filter("type = 'other'").count()); - verificationDataset.show(false); - -//TODO verify value and name of the fields for vocab related value (i.e. accessright, bestaccessright) } @@ -388,7 +878,6 @@ public class DumpJobTest { DumpProducts dump = new DumpProducts(); dump .run( - // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, CommunityResult.class, Constants.DUMPTYPE.COMMUNITY.getType()); @@ -408,4 +897,51 @@ public class DumpJobTest { } + @Test + public void testArticlePCA() { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultDump/publication_pca") + .getPath(); + + final String communityMapPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/communityMapPath/communitymap.json") + .getPath(); + + DumpProducts dump = new DumpProducts(); + dump + .run( + // false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + false, sourcePath, workingDir.toString() + "/result", communityMapPath, Publication.class, + GraphResult.class, Constants.DUMPTYPE.COMPLETE.getType()); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, GraphResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(GraphResult.class)); + + Assertions.assertEquals(23, verificationDataset.count()); + + Assertions.assertEquals(23, verificationDataset.filter("type = 'publication'").count()); + + verificationDataset.createOrReplaceTempView("check"); + + org.apache.spark.sql.Dataset temp = spark + .sql( + "select id " + + "from check " + + "lateral view explode (instance) i as inst " + + "where inst.articleprocessingcharge is not null"); + + Assertions.assertTrue(temp.count() == 2); + + Assertions.assertTrue(temp.filter("id = '50|datacite____::05c611fdfc93d7a2a703d1324e28104a'").count() == 1); + + Assertions.assertTrue(temp.filter("id = '50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8'").count() == 1); + + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java index 03eed7a45..86d2f93c9 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/PrepareResultProjectJobTest.java @@ -223,4 +223,102 @@ public class PrepareResultProjectJobTest { } + @Test + public void testMatchValidated() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/resultProject/match_validatedRels") + .getPath(); + + SparkPrepareResultProject.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/preparedInfo", + "-sourcePath", sourcePath + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/preparedInfo") + .map(item -> OBJECT_MAPPER.readValue(item, ResultProject.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(ResultProject.class)); + + assertEquals(2, verificationDataset.count()); + + assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); + assertEquals( + 1, + verificationDataset.filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); + + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select resultId, MyT.id project , MyT.title title, MyT.acronym acronym , MyT.provenance.provenance provenance, " + + + "MyT.validated.validatedByFunder, MyT.validated.validationDate " + + "from dataset " + + "lateral view explode(projectsList) p as MyT "; + + org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); + assertEquals(3, resultExplodedProvenance.count()); + assertEquals(3, resultExplodedProvenance.filter("validatedByFunder = true").count()); + assertEquals( + 2, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter("resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'") + .count()); + + assertEquals( + 2, + resultExplodedProvenance + .filter("project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true " + + "and validationDate = '2021-08-06'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::0f7d119de1f656b5763a16acf876fed6' " + + "and resultId = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80' " + + "and validatedByFunder = true and validationDate = '2021-08-04'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter("project = '40|aka_________::03376222b28a3aebf2730ac514818d04'") + .count()); + + assertEquals( + 1, + resultExplodedProvenance + .filter( + "project = '40|aka_________::03376222b28a3aebf2730ac514818d04' " + + "and resultId = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb' " + + "and validatedByFunder = true and validationDate = '2021-08-05'") + .count()); + + assertEquals( + 3, resultExplodedProvenance.filter("provenance = 'sysimport:crosswalk:entityregistry'").count()); + + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java index 98902b618..8391c8963 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/QueryInformationSystemTest.java @@ -25,7 +25,7 @@ class QueryInformationSystemTest { private static final String XQUERY = "for $x in collection('/db/DRIVER/ContextDSResources/ContextDSResourceType') " + " where $x//CONFIGURATION/context[./@type='community' or ./@type='ri'] " + - " and ($x//context/param[./@name = 'status']/text() = 'manager' or $x//context/param[./@name = 'status']/text() = 'all') " + " and ($x//context/param[./@name = 'status']/text() = 'all') " + " return " + " " + @@ -71,7 +71,7 @@ class QueryInformationSystemTest { lenient().when(isLookUpService.quickSearchProfile(XQUERY)).thenReturn(communityMap); queryInformationSystem = new QueryInformationSystem(); queryInformationSystem.setIsLookUp(isLookUpService); - map = queryInformationSystem.getCommunityMap(); + map = queryInformationSystem.getCommunityMap(false, null); } @Test diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java index e6f0e9106..4209caad3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/SplitForCommunityTest.java @@ -79,7 +79,7 @@ public class SplitForCommunityTest { final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); JavaRDD tmp = sc - .textFile(workingDir.toString() + "/split/dh-ch") + .textFile(workingDir.toString() + "/split/Digital_Humanities_and_Cultural_Heritage") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); org.apache.spark.sql.Dataset verificationDataset = spark @@ -92,7 +92,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|dedup_wf_001::51b88f272ba9c3bb181af64e70255a80'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/egi") + .textFile(workingDir.toString() + "/split/EGI_Federation") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark @@ -105,7 +105,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|dedup_wf_001::e4805d005bfab0cd39a1642cbf477fdb'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/ni") + .textFile(workingDir.toString() + "/split/Neuroinformatics") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark @@ -118,7 +118,7 @@ public class SplitForCommunityTest { 1, verificationDataset.filter("id = '50|datacite____::6b1e3a2fa60ed8c27317a66d6357f795'").count()); tmp = sc - .textFile(workingDir.toString() + "/split/science-innovation-policy") + .textFile(workingDir.toString() + "/split/Science_and_Innovation_Policy_Studies") .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); verificationDataset = spark diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java index a164593ec..9710e4553 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/UpdateProjectInfoTest.java @@ -5,11 +5,15 @@ import java.io.IOException; import java.nio.file.Files; import java.nio.file.Path; import java.util.HashMap; +import java.util.logging.Filter; +import java.util.stream.Collectors; import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.FilterFunction; +import org.apache.spark.api.java.function.MapFunction; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; import org.apache.spark.sql.SparkSession; @@ -25,6 +29,8 @@ import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.oa.graph.dump.community.SparkUpdateProjectInfo; import eu.dnetlib.dhp.schema.dump.oaf.Result; import eu.dnetlib.dhp.schema.dump.oaf.community.CommunityResult; +import eu.dnetlib.dhp.schema.dump.oaf.community.Funder; +import eu.dnetlib.dhp.schema.dump.oaf.community.Project; public class UpdateProjectInfoTest { @@ -135,4 +141,96 @@ public class UpdateProjectInfoTest { resultExplodedProvenance.show(false); } + @Test + public void testValidatedRelation() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/addProjectInfo") + .getPath(); + + SparkUpdateProjectInfo.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-preparedInfoPath", sourcePath + "/preparedInfoValidated", + "-outputPath", workingDir.toString() + "/result", + "-sourcePath", sourcePath + "/publication_extendedmodel" + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/result") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(CommunityResult.class)); + + verificationDataset.show(false); + + Assertions.assertEquals(2, verificationDataset.count()); + verificationDataset.createOrReplaceTempView("dataset"); + + String query = "select id, MyT.code code, MyT.title title, MyT.funder.name funderName, MyT.funder.shortName funderShortName, " + + + "MyT.funder.jurisdiction funderJurisdiction, MyT.funder.fundingStream fundingStream, MyT.validated " + + "from dataset " + + "lateral view explode(projects) p as MyT "; + + org.apache.spark.sql.Dataset resultExplodedProvenance = spark.sql(query); + + Assertions.assertEquals(2, resultExplodedProvenance.count()); + resultExplodedProvenance.show(false); + + Assertions + .assertEquals( + 2, + resultExplodedProvenance.filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2'").count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '123455'") + .count()); + + Assertions + .assertEquals( + 1, + resultExplodedProvenance + .filter("id = '50|pensoft_____::00ea4a1cd53806a97d62ea6bf268f2a2' and code = '119027'") + .count()); + + Project project = verificationDataset + .map( + (MapFunction) cr -> cr + .getProjects() + .stream() + .filter(p -> p.getValidated() != null) + .collect(Collectors.toList()) + .get(0), + Encoders.bean(Project.class)) + .first(); + + Assertions.assertTrue(project.getFunder().getName().equals("Academy of Finland")); + Assertions.assertTrue(project.getFunder().getShortName().equals("AKA")); + Assertions.assertTrue(project.getFunder().getJurisdiction().equals("FI")); + Assertions.assertTrue(project.getFunder().getFundingStream() == null); + Assertions.assertTrue(project.getValidated().getValidationDate().equals("2021-08-06")); + + project = verificationDataset + .map( + (MapFunction) cr -> cr + .getProjects() + .stream() + .filter(p -> p.getValidated() == null) + .collect(Collectors.toList()) + .get(0), + Encoders.bean(Project.class)) + .first(); + + Assertions.assertTrue(project.getFunder().getName().equals("European Commission")); + Assertions.assertTrue(project.getFunder().getShortName().equals("EC")); + Assertions.assertTrue(project.getFunder().getJurisdiction().equals("EU")); + Assertions.assertTrue(project.getFunder().getFundingStream().equals("H2020")); + + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java index 69e550d45..d2343d274 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/CreateRelationTest.java @@ -14,6 +14,7 @@ import com.google.gson.Gson; import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.dump.oaf.graph.Relation; import eu.dnetlib.dhp.schema.oaf.Datasource; +import eu.dnetlib.dhp.schema.oaf.Project; import eu.dnetlib.dhp.utils.DHPUtils; class CreateRelationTest { @@ -203,6 +204,7 @@ class CreateRelationTest { " \n" + " oac_ni\n" + " 2018-03-01T12:00:00\n" + + " \n" + " \n" + " \n" + " re3data_____::5b9bf9171d92df854cf3c520692e9122\n" + @@ -376,7 +378,7 @@ class CreateRelationTest { " \n" + " 675858\n" + " \n" + - " H2020-EINFRA-2015-1\n" + + " EC | H2020 | RIA\n" + " EC\n" + " West-Life\n" + " \n" + @@ -437,7 +439,65 @@ class CreateRelationTest { " \n" + " oaa_elixir-gr\n" + " 2018-03-01T12:00:00\n" + - " \n" + + " \n" + + " \n" + + " BIO-INFORMATICS RESEARCH NETWORK COORDINATING CENTER (BIRN-CC)\n" + + + " \n" + + " 1U24RR025736-01\n" + + " NIH\n" + + " \n" + + " \n" + + " COLLABORATIVE RESEARCH: The Cognitive Neuroscience of Category Learning\n" + + + " \n" + + " 0223843\n" + + " NSF\n" + + " \n" + + " \n" + + " The Cognitive Atlas: Developing an Interdisciplinary Knowledge Base Through Socia\n" + + + " \n" + + " 5R01MH082795-05\n" + + " NIH\n" + + " \n" + + " \n" + + " Fragmented early life environmental and emotional / cognitive vulnerabilities\n" + + + " \n" + + " 1P50MH096889-01A1\n" + + " NIH\n" + + " \n" + + " \n" + + " Enhancement of the 1000 Functional Connectome Project\n" + + + " \n" + + " 1R03MH096321-01A1\n" + + " TUBITAK\n" + + " \n" + + " \n" + + " CRCNS Data Sharing: An open data repository for cognitive neuroscience: The OpenfMRI Project\n" + + + " \n" + + " 1131441\n" + + " NSF\n" + + " \n" + + " \n" + + " Enhancing Human Cortical Plasticity: Visual Psychophysics and fMRI\n" + + + " \n" + + " 0121950\n" + + " NSF\n" + + " \n" + + " \n" + + " Transforming statistical methodology for neuroimaging meta-analysis.\n" + + + " \n" + + " 100309\n" + + " WT\n" + + " \n" + + " " + + " \n" + " \n" + @@ -566,4 +626,98 @@ class CreateRelationTest { tmp.contains("10|doajarticles::2899208a99aa7d142646e0a80bfeef05")); } + + @Test + public void test2() { + List cInfoList = new ArrayList<>(); + final Consumer consumer = ci -> cInfoList.add(ci); + + queryInformationSystem + .getContextRelation(consumer, "projects", ModelSupport.getIdPrefix(Project.class)); + + cInfoList.forEach(c -> System.out.println(new Gson().toJson(c))); + + List rList = new ArrayList<>(); + + cInfoList.forEach(cInfo -> Process.getRelation(cInfo).forEach(rList::add)); + + Assertions.assertEquals(44, rList.size()); + + Assertions + .assertFalse( + rList + .stream() + .map(r -> r.getSource().getId()) + .collect(Collectors.toSet()) + .contains( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("dh-ch")))); + + Assertions + .assertEquals( + 2, + rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .collect(Collectors.toList()) + .size()); + + Assertions + .assertEquals( + 2, + rList + .stream() + .filter( + r -> r + .getTarget() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .collect(Collectors.toList()) + .size()); + + Set tmp = rList + .stream() + .filter( + r -> r + .getSource() + .getId() + .equals( + String + .format( + "%s|%s::%s", Constants.CONTEXT_ID, + Constants.CONTEXT_NS_PREFIX, + DHPUtils.md5("clarin")))) + .map(r -> r.getTarget().getId()) + .collect(Collectors.toSet()); + + Assertions + .assertTrue( + tmp.contains("40|corda__h2020::b5a4eb56bf84bef2ebc193306b4d423f") && + tmp.contains("40|corda_______::ef782b2d85676aa3e5a907427feb18c4")); + + rList.forEach(rel -> { + if (rel.getSource().getId().startsWith("40|")) { + String proj = rel.getSource().getId().substring(3); + Assertions.assertTrue(proj.substring(0, proj.indexOf("::")).length() == 12); + } + }); + + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java index 69100a114..80b5fd89e 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpOrganizationProjectDatasourceTest.java @@ -22,6 +22,7 @@ import org.slf4j.LoggerFactory; import com.fasterxml.jackson.databind.ObjectMapper; +import eu.dnetlib.dhp.oa.graph.dump.exceptions.NoAvailableEntityTypeException; import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.Organization; import eu.dnetlib.dhp.schema.oaf.Project; @@ -88,7 +89,7 @@ public class DumpOrganizationProjectDatasourceTest { org.apache.spark.sql.Dataset verificationDataset = spark .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.dump.oaf.graph.Organization.class)); - Assertions.assertEquals(34, verificationDataset.count()); + Assertions.assertEquals(15, verificationDataset.count()); verificationDataset .foreach( @@ -98,7 +99,7 @@ public class DumpOrganizationProjectDatasourceTest { } @Test - public void dumpProjectTest() { + public void dumpProjectTest() throws NoAvailableEntityTypeException { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/project") @@ -127,7 +128,7 @@ public class DumpOrganizationProjectDatasourceTest { } @Test - public void dumpDatasourceTest() { + public void dumpDatasourceTest() throws NoAvailableEntityTypeException { final String sourcePath = getClass() .getResource("/eu/dnetlib/dhp/oa/graph/dump/complete/datasource") .getPath(); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java index d80eb3ec6..fe178795d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/DumpRelationTest.java @@ -10,6 +10,7 @@ import org.apache.commons.io.FileUtils; import org.apache.spark.SparkConf; import org.apache.spark.api.java.JavaRDD; import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; import org.apache.spark.sql.Dataset; import org.apache.spark.sql.Encoders; import org.apache.spark.sql.Row; @@ -71,7 +72,7 @@ public class DumpRelationTest { public void test1() throws Exception { final String sourcePath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation") .getPath(); SparkDumpRelationJob.main(new String[] { @@ -93,6 +94,9 @@ public class DumpRelationTest { verificationDataset.createOrReplaceTempView("table"); + verificationDataset + .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + Dataset check = spark .sql( "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " @@ -127,4 +131,76 @@ public class DumpRelationTest { .count()); } + @Test + public void test2() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/relation/relation_validated") + .getPath(); + + SparkDumpRelationJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath + }); + +// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(Relation.class)); + + verificationDataset.createOrReplaceTempView("table"); + + verificationDataset + .foreach((ForeachFunction) r -> System.out.println(new ObjectMapper().writeValueAsString(r))); + + Dataset check = spark + .sql( + "SELECT reltype.name, source.id source, source.type stype, target.id target,target.type ttype, provenance.provenance " + + + "from table "); + + Assertions.assertEquals(20, check.filter("name = 'isProvidedBy'").count()); + Assertions + .assertEquals( + 20, check + .filter( + "name = 'isProvidedBy' and stype = 'datasource' and ttype = 'organization' and " + + "provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(7, check.filter("name = 'isParticipant'").count()); + Assertions + .assertEquals( + 7, check + .filter( + "name = 'isParticipant' and stype = 'organization' and ttype = 'project' " + + "and provenance = 'Harvested'") + .count()); + + Assertions.assertEquals(1, check.filter("name = 'isAuthorInstitutionOf'").count()); + Assertions + .assertEquals( + 1, check + .filter( + "name = 'isAuthorInstitutionOf' and stype = 'organization' and ttype = 'result' " + + "and provenance = 'Inferred by OpenAIRE'") + .count()); + + Assertions.assertEquals(2, check.filter("name = 'isProducedBy'").count()); + Assertions + .assertEquals( + 2, check + .filter( + "name = 'isProducedBy' and stype = 'project' and ttype = 'result' " + + "and provenance = 'Harvested' and validated = true " + + "and validationDate = '2021-08-06'") + .count()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java index 049959704..08fcd49a8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/QueryInformationSystemTest.java @@ -13,6 +13,7 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @@ -528,7 +529,8 @@ class QueryInformationSystemTest { List cInfoList = new ArrayList<>(); final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.execContextRelationQuery(); - queryInformationSystem.getContextRelation(consumer, "contentproviders", "10|"); + queryInformationSystem + .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); Assertions.assertEquals(5, cInfoList.size()); } @@ -539,7 +541,8 @@ class QueryInformationSystemTest { List cInfoList = new ArrayList<>(); final Consumer consumer = ci -> cInfoList.add(ci); queryInformationSystem.execContextRelationQuery(); - queryInformationSystem.getContextRelation(consumer, "contentproviders", "10"); + queryInformationSystem + .getContextRelation(consumer, "contentproviders", ModelSupport.entityIdPrefix.get("datasource")); cInfoList.forEach(contextInfo -> { switch (contextInfo.getId()) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java new file mode 100644 index 000000000..3e4ab93c5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/complete/SelectRelationTest.java @@ -0,0 +1,100 @@ + +package eu.dnetlib.dhp.oa.graph.dump.complete; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.HashMap; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.ForeachFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.Relation; +import net.sf.saxon.expr.instruct.ForEach; + +public class SelectRelationTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory + .getLogger(SelectRelationTest.class); + + private static HashMap map = new HashMap<>(); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SelectRelationTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SelectRelationTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SelectRelationTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void test1() throws Exception { + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/selectrelations") + .getPath(); + + SparkSelectValidRelationsJob.main(new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-outputPath", workingDir.toString() + "/relation", + "-sourcePath", sourcePath + }); + +// dumpCommunityProducts.exec(MOCK_IS_LOOK_UP_URL,Boolean.FALSE, workingDir.toString()+"/dataset",sourcePath,"eu.dnetlib.dhp.schema.oaf.Dataset","eu.dnetlib.dhp.schema.dump.oaf.Dataset"); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/relation") + .map(item -> OBJECT_MAPPER.readValue(item, eu.dnetlib.dhp.schema.oaf.Relation.class)); + + org.apache.spark.sql.Dataset verificationDataset = spark + .createDataset(tmp.rdd(), Encoders.bean(eu.dnetlib.dhp.schema.oaf.Relation.class)); + + Assertions.assertTrue(verificationDataset.count() == 7); + + } + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java index d1e3b3acc..4967ae5a5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/ResultLinkedToProjectTest.java @@ -75,8 +75,8 @@ public class ResultLinkedToProjectTest { .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/papers.json") .getPath(); - final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch/relations.json") + final String graphPath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/nomatch") .getPath(); SparkResultLinkedToProject.main(new String[] { @@ -84,7 +84,7 @@ public class ResultLinkedToProjectTest { "-outputPath", workingDir.toString() + "/preparedInfo", "-sourcePath", sourcePath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + "-graphPath", graphPath }); @@ -109,7 +109,7 @@ public class ResultLinkedToProjectTest { .getPath(); final String relationPath = getClass() - .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match/relations.json") + .getResource("/eu/dnetlib/dhp/oa/graph/dump/funderresource/match") .getPath(); SparkResultLinkedToProject.main(new String[] { @@ -117,7 +117,7 @@ public class ResultLinkedToProjectTest { "-outputPath", workingDir.toString() + "/preparedInfo", "-sourcePath", sourcePath, "-resultTableName", "eu.dnetlib.dhp.schema.oaf.Publication", - "-relationPath", relationPath + "-graphPath", relationPath }); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java index 8ac0c552f..477481c08 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/dump/funderresult/SplitPerFunderTest.java @@ -75,7 +75,7 @@ public class SplitPerFunderTest { "-isSparkSessionManaged", Boolean.FALSE.toString(), "-outputPath", workingDir.toString() + "/split", "-sourcePath", sourcePath, - "-relationPath", sourcePath + "-graphPath", sourcePath }); @@ -137,5 +137,17 @@ public class SplitPerFunderTest { .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); Assertions.assertEquals(3, tmp.count()); + // MZOS 1 + tmp = sc + .textFile(workingDir.toString() + "/split/MZOS") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(1, tmp.count()); + + // CONICYT 0 + tmp = sc + .textFile(workingDir.toString() + "/split/CONICYTF") + .map(item -> OBJECT_MAPPER.readValue(item, CommunityResult.class)); + Assertions.assertEquals(0, tmp.count()); + } } diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala new file mode 100644 index 000000000..c22243f94 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/resolution/ResolveEntitiesTest.scala @@ -0,0 +1,233 @@ +package eu.dnetlib.dhp.oa.graph.resolution + + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.schema.common.EntityType +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils +import eu.dnetlib.dhp.schema.oaf.{Publication, Result, StructuredProperty} +import org.apache.commons.io.FileUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql._ +import org.junit.jupiter.api.Assertions._ +import org.junit.jupiter.api.TestInstance.Lifecycle +import org.junit.jupiter.api.{AfterAll, BeforeAll, Test, TestInstance} + +import java.nio.file.{Files, Path} +import scala.collection.JavaConverters._ +import scala.io.Source + +@TestInstance(Lifecycle.PER_CLASS) +class ResolveEntitiesTest extends Serializable { + + var workingDir:Path = null + + val FAKE_TITLE = "FAKETITLE" + val FAKE_SUBJECT = "FAKESUBJECT" + + var sparkSession:Option[SparkSession] = None + + + @BeforeAll + def setUp() :Unit = { + workingDir = Files.createTempDirectory(getClass.getSimpleName) + + val conf = new SparkConf() + sparkSession = Some(SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master("local[*]").getOrCreate()) + populateDatasets(sparkSession.get) + generateUpdates(sparkSession.get) + + } + + + @AfterAll + def tearDown():Unit = { + FileUtils.deleteDirectory(workingDir.toFile) + sparkSession.get.stop() + + + } + + + def generateUpdates(spark:SparkSession):Unit = { + val template = Source.fromInputStream(this.getClass.getResourceAsStream("updates")).mkString + + + val pids:List[String] = template.lines.map{id => + val r = new Result + r.setId(id.toLowerCase.trim) + r.setSubject(List(OafMapperUtils.structuredProperty(FAKE_SUBJECT, OafMapperUtils.qualifier("fos","fosCS", "fossSchema", "fossiFIgo"), null)).asJava) + r.setTitle(List(OafMapperUtils.structuredProperty(FAKE_TITLE, OafMapperUtils.qualifier("fos","fosCS", "fossSchema", "fossiFIgo"), null)).asJava) + r + }.map{r => + val mapper = new ObjectMapper() + + mapper.writeValueAsString(r)}.toList + + + val sc =spark.sparkContext + + println(sc.parallelize(pids).count()) + + spark.createDataset(sc.parallelize(pids))(Encoders.STRING).write.mode(SaveMode.Overwrite).option("compression", "gzip").text(s"$workingDir/updates") + + + + + + import spark.implicits._ + implicit val resEncoder: Encoder[Result] = Encoders.bean(classOf[Result]) + val ds = spark.read.text(s"$workingDir/updates").as[String].map{s => val mapper = new ObjectMapper() + mapper.readValue(s, classOf[Result])}.collect() + + + + + assertEquals(4, ds.length) + ds.foreach{r => assertNotNull(r.getSubject)} + ds.foreach{r => assertEquals(1,r.getSubject.size())} + ds.foreach{r => assertNotNull(r.getTitle)} + ds.foreach{r => assertEquals(1,r.getTitle.size())} + + + + ds.flatMap(r => r.getTitle.asScala.map(t => t.getValue)).foreach(t => assertEquals(FAKE_TITLE,t)) + ds.flatMap(r => r.getSubject.asScala.map(t => t.getValue)).foreach(t => assertEquals(FAKE_SUBJECT,t)) + + println("generated Updates") + } + + + def populateDatasets(spark:SparkSession):Unit = { + import spark.implicits._ + val entities =SparkResolveEntities.entities + + entities.foreach{ + e => + val template = Source.fromInputStream(this.getClass.getResourceAsStream(s"$e")).mkString + spark.createDataset(spark.sparkContext.parallelize(template.lines.toList)).as[String].write.option("compression", "gzip").text(s"$workingDir/graph/$e") + println(s"Created Dataset $e") + } + SparkResolveRelation.extractPidResolvedTableFromJsonRDD(spark, s"$workingDir/graph", s"$workingDir/work") + + } + + + @Test + def testResolution():Unit = { + val spark:SparkSession = sparkSession.get + implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + SparkResolveEntities.resolveEntities(spark,s"$workingDir/work", s"$workingDir/updates" ) + + val ds = spark.read.load(s"$workingDir/work/resolvedEntities").as[Result] + + assertEquals(3, ds.count()) + + ds.collect().foreach{ + r => + assertTrue(r.getId.startsWith("50")) + } + } + + + + + private def structuredPContainsValue(l:java.util.List[StructuredProperty], exptectedValue:String):Boolean = { + l.asScala.exists(p =>p.getValue!= null && p.getValue.equalsIgnoreCase(exptectedValue)) + } + + @Test + def testUpdate():Unit = { + val spark:SparkSession = sparkSession.get + import spark.implicits._ + implicit val resEncoder: Encoder[Result] = Encoders.kryo(classOf[Result]) + val m = new ObjectMapper() + SparkResolveEntities.resolveEntities(spark,s"$workingDir/work", s"$workingDir/updates" ) + SparkResolveEntities.generateResolvedEntities(spark,s"$workingDir/work",s"$workingDir/graph", s"$workingDir/target" ) + + + + val pubDS:Dataset[Result] = spark.read.text(s"$workingDir/target/publication").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.publication)) + val t = pubDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() + + + var ct = pubDS.count() + var et = pubDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count() + + assertEquals(ct, et) + + + + val datDS:Dataset[Result] = spark.read.text(s"$workingDir/target/dataset").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.dataset)) + val td = datDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() + ct = datDS.count() + et = datDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count() + assertEquals(ct, et) + + + val softDS:Dataset[Result] = spark.read.text(s"$workingDir/target/software").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.software)) + val ts = softDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() + ct = softDS.count() + et = softDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count() + assertEquals(ct, et) + + + val orpDS:Dataset[Result] = spark.read.text(s"$workingDir/target/otherresearchproduct").as[String].map(s => SparkResolveEntities.deserializeObject(s, EntityType.otherresearchproduct)) + val to = orpDS.filter(p => p.getTitle!=null && p.getSubject!=null).filter(p => p.getTitle.asScala.exists(t => t.getValue.equalsIgnoreCase("FAKETITLE"))).count() + + + ct = orpDS.count() + et = orpDS.filter(p => p.getTitle!= null && p.getTitle.asScala.forall(t => t.getValue != null && t.getValue.nonEmpty)).count() + assertEquals(ct, et) + + + + + + assertEquals(0, t) + assertEquals(2, td) + assertEquals(1, ts) + assertEquals(0, to) + + } + + + + + + @Test + def testMerge():Unit = { + + val r = new Result + r.setSubject(List(OafMapperUtils.structuredProperty(FAKE_SUBJECT, OafMapperUtils.qualifier("fos","fosCS", "fossSchema", "fossiFIgo"), null)).asJava) + + val mapper = new ObjectMapper() + + val p = mapper.readValue(Source.fromInputStream(this.getClass.getResourceAsStream(s"publication")).mkString.lines.next(), classOf[Publication]) + + + r.mergeFrom(p) + + + println(mapper.writeValueAsString(r)) + + + + + + + + + } + + + + + + + + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala index 5b7fbe1cf..bd7e4fd09 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/graph/scholix/ScholixGraphTest.scala @@ -1,10 +1,10 @@ package eu.dnetlib.dhp.sx.graph.scholix import com.fasterxml.jackson.databind.{DeserializationFeature, ObjectMapper, SerializationFeature} +import eu.dnetlib.dhp.oa.graph.resolution.SparkResolveRelation import eu.dnetlib.dhp.schema.oaf.{Relation, Result} import eu.dnetlib.dhp.schema.sx.scholix.Scholix import eu.dnetlib.dhp.schema.sx.summary.ScholixSummary -import eu.dnetlib.dhp.sx.graph.SparkResolveRelation import eu.dnetlib.dhp.sx.graph.bio.pubmed.AbstractVocabularyTest import org.json4s import org.json4s.DefaultFormats diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json new file mode 100644 index 000000000..061145d0f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/doiboostpub.json @@ -0,0 +1 @@ +{"context": [], "dataInfo": {"invisible": false, "trust": "0.9", "provenanceaction": {"classid": "sysimport:actionset", "classname": "sysimport:actionset", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "inferred": false, "deletedbyinference": false}, "resourcetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}, "pid": [{"qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1097/00132586-197308000-00003"}], "contributor": [], "bestaccessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "relevantdate": [{"qualifier": {"classid": "created", "classname": "created", "schemeid": "dnet:dataCite_date", "schemename": "dnet:dataCite_date"}, "value": "2006-11-06T11:36:37Z"}], "collectedfrom": [{"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}], "id": "50|doi_________::b0baa0eb88a5788f0b8815560d2a32f2", "subject": [], "lastupdatetimestamp": 1620353302565, "author": [{"fullname": "N. S. AGRUSS", "surname": "AGRUSS", "name": "N. S.", "rank": 1}, {"fullname": "E. Y. ROSIN", "surname": "ROSIN", "name": "E. Y.", "rank": 2}, {"fullname": "R. J. ADOLPH", "surname": "ADOLPH", "name": "R. J.", "rank": 3}, {"fullname": "N. O. FOWLER", "surname": "FOWLER", "name": "N. O.", "rank": 4}], "instance": [{"hostedby": {"key": "10|issn___print::b8cee613d4f898f8c03956d57ea69be2", "value": "Survey of Anesthesiology"}, "url": ["https://doi.org/10.1097/00132586-197308000-00003"], "pid": [{"qualifier": {"classid": "doi", "classname": "doi", "schemeid": "dnet:pid_types", "schemename": "dnet:pid_types"}, "value": "10.1097/00132586-197308000-00003"}], "dateofacceptance": {"value": "2006-11-06T11:36:37Z"}, "collectedfrom": {"key": "10|openaire____::081b82f96300b6a6e3d282bad31cb6e2", "value": "Crossref"}, "accessright": {"classid": "UNKNOWN", "classname": "not available", "schemeid": "dnet:access_modes", "schemename": "dnet:access_modes"}, "instancetype": {"classid": "0001", "classname": "Article", "schemeid": "dnet:publication_resource", "schemename": "dnet:publication_resource"}}], "dateofcollection": "2021-05-07T02:08:22Z", "fulltext": [], "description": [], "format": [], "journal": {"issnPrinted": "0039-6206", "vol": "17", "sp": "304", "name": "Survey of 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Vertical velocities can be estimated indirectly from in situ observations by theoretical frameworks like the-equation. Direct measures of vertical exchanges are challenging due to their typically ephemeral spatiotemporal scales. In this study we address this problem with an adaptive sampling strategy coupling various biophysical instruments. We analyze the 3-D organization of a cyclonic mesoscale structure finely sampled during the Observing Submesoscale Coupling At High Resolution cruise in the Ligurian Sea during fall 2015. The observations, acquired with a moving vessel profiler, highlight a subsurface low-salinity layer (≃50 m), as well as rising isopycnals, generated by geostrophic cyclonic circulation, in the structure's center. Reconstructed 3-D fields of density and horizontal velocities are used to estimate the vertical velocity field down to 250 m by applying the adiabatic QG-equation, for the first time in this region. The vertical motions are characterized by multipolar patterns of downward and upward velocities on the edges of the structure and significantly smaller vertical velocities in its center. Both the 3-D distribution of particles (size ≥100 μm), measured with a laser optical plankton counter, and the Synechococcus and Prochlorococcus abundances (cell per cubic meter) measured by flow cytometry are consistent with the 3-D velocity field. In particular, a secondary vertical recirculation is identified that upwells particles (from 250 to 100 m) along isohalines to the structure's center. Besides demonstrating the effect of vertical patterns on biogeochemical distributions, this case study suggests to use particle matter as a tracer to assess physical dynamics."],"format":["application/pdf"],"id":"50|dedup_wf_001::0d16b1714ab3077df73893a8ea57d776","instance":[{"accessright":{"code":"c_abf2","label":"OPEN","scheme":"http://vocabularies.coar-repositories.org/documentation/access_rights/"},"collectedfrom":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en Ligne"},"hostedby":{"key":"10|opendoar____::7e7757b1e12abcb736ab9a754ffb617a","value":"Hyper Article en 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Personality traits, affective status and stress are some of the relevant factors contributing to lower quality of life and symptom exacerbation in IBS patients. In order to examine the role of stress in IBS symptom exacerbation, the aims of this study were to explore the relationship of daily stressful events and symptom severity in a prospective manner and to explore the roles of neuroticism, anxiety, depression and stress in the vicious circle of symptom perpetuation. A total of 49 patients with IBS reported their symptom severity and daily stressful events intensity each day for 14 consecutive days. They also completed the Big five personality inventory, the Beck Depression Inventory and the State-trait anxiety inventory. Cross-correlation analyses were performed on the time series data for daily stress and symptom severity for each participant separately. Four different patterns of relationships were found in different subgroups of participants: positive cross-correlations of symptom severity and stress intensity on the same day; higher symptom severity on days following stressful days; lower symptom severity on days following stressful days; and lower stress intensity on days following severe symptoms. Using average scores for daily stress and symptom severity, as well as scores for neuroticism, anxiety and depression, we performed a path analysis to test a model of symptom exacerbation. It showed that, on the group level, average stress intensity predicts average symptom severity. Neuroticism and anxiety were not significant predictors of symptom severity, while depression showed a marginally significant relationship with symptom severity, mediated by stress intensity. In conclusion, depression and daily stress seem to be important contributors to the vicious circle of IBS symptom perpetuation.","Síndrome del intestino irritable se considera un trastorno biopsicosocial, el resultado de la combinación compleja de factores predisponentes, precipitantes y perpetuos. Rasgos de personalidad, estado afectivo y estrés son algunos de los factores relevantes que contribuyen a la calidad de vida más baja y la exacerbación sintomática de los pacientes con SII. Para examinar el papel del estrés en la exacerbación sintomática de SII, el objetivo de este estudio era explorar la relación entre los acontecimientos cotidianos estresantes y la intensidad de los síntomas de forma prospectiva, tanto como explorar los papeles del neuroticismo, ansiedad, depresión y estrés en el círculo vicioso de perpetuación de los síntomas. Todos los 49 pacientes con SII informaron sobre la intensidad de los síntomas y la intensidad de los acontecimientos cotidianos estresantes cada día durante 14 días consecutivos. Además, completaron el Test de personalidad de los cinco grandes, Inventario de depresión de Beck e Inventario de ansiedad estado-rasgo. En los datos de series temporales se hizo el análisis de correlación cruzada para la intensidad del estrés diario y de los síntomas para cada participante por separado. Se encontraron cuatro patrones de relación diferentes en diferentes subgrupos de participantes: correlación cruzada positiva de la intensidad de los síntomas y del estrés el mismo día; intensidad de los síntomas más alta en los días después de los días estresantes; intensidad de los síntomas más baja en los días después de los días estresantes e intensidad del estrés más baja en los días después de los síntomas graves. Usando resultados promedios para el estrés diario y la intensidad de los síntomas, tanto como resultados para el neuroticismo, ansiedad y depresión, realizamos un análisis del camino para examinar el modelo de la exacerbación de los síntomas. Mostró que, al nivel de grupo, la intensidad del estrés promedia predice la intensidad de los síntomas promedia. Neuroticismo y ansiedad no eran predictores significativos de la intensidad de los síntomas, mientras que la depresión demostró una relación marginalmente significante con la intensidad de los síntomas, mediada por la intensidad del estrés. 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Among them the Habitat (92/43/EC) and Bird Directives (79/409/EC), the Water Framework Directive (2000/60/EC), and the Noise Directive (2002/49/EC) have led to the evaluation/designation of areas in Europe with different criteria. In this study our goal was to understand how the ES capacity of an area is related to its designation and if areas with multiple designations have higher capacity in providing ES. We selected four catchments in Greece with a great variety of characteristics covering over 25% of the national territory. Inside the catchments we assessed the ES capacity (following the methodology of Burkhard et al. 2009) of areas designated as Natura 2000 sites, Quiet areas and Wetlands or Water bodies and found those areas that have multiple designations. Data were analyzed by GLM to reveal differences regarding the ES capacity among the different types of areas. We also investigated by PCA synergies and trade-offs among different kinds of ES and tested for correlations among landscape properties, such as elevation, aspect and slope and the ES potential. Our results show that areas with different types or multiple designations have a different capacity in providing ES. Areas of one designation type (Protected or Quiet Areas) had in general intermediate scores in most ES but scores were higher compared to areas with no designation, which displayed stronger capacity in provisioning services. Among Protected Areas and Quiet Areas the latter scored better in general. Areas that combined both designation types (Protected and Quiet Areas) showed the highest capacity in 13 out of 29 ES, that were mostly linked with natural and forest ecosystems. We found significant synergies among most regulating, supporting and cultural ES which in turn display trade-offs with provisioning services. The different ES are spatially related and display strong correlation with landscape properties, such as elevation and slope. We suggest that the designation status of an area can be used as an alternative tool for environmental policy, indicating the capacity for ES provision. Multiple designations of areas can be used as proxies for locating ES “hotspots”. 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simulacija; usklađivanje oblika; opruge i mase"}],"title":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Simulacija elastičnih objekata"},{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"value":"Soft bodies simulation"}],"tool":[]} +{"author":[{"affiliation":[],"fullname":"Sobočanec, Sandra","name":"Sandra","pid":[],"rank":1,"surname":"Sobočanec"}],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"}],"contactgroup":[],"contactperson":[],"context":[],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2006-01-01"},"dateofcollection":"2021-10-25T05:50:25+0000","dateoftransformation":"2021-10-26T05:22:35.748Z","description":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Propolis je tijekom stoljeća, a u posljednje vrijeme i u suvremenoj medicinskoj praksi ispitivan i korišten kao protuvirusno, protubakterijsko i protugljivično sredstvo. Biološki učinci propolisa vezani su uz antibiotska, protuupalna i antioksidacijska svojstva. Jedan od sastojaka propolisa su flavonoidi, čija je karakteristika visoki antioksidacijski potencijal zbog kojeg im se pripisuje sposobnost prevencije različitih bolesti kao što su različite vrste tumora, osteoporoza, kardiovaskularne i neurodegenerativne bolesti. U našim ispitivanjima koristili smo nativni propolis u dvije doze (100 mg kg-1, 300 mg kg-1), kojem smo istražili sastav, udio i vrstu flavonoida odgovornih za njegov oksidacijski/antioksidacijski učinak. Krizin je bio prisutan u najvećoj koncentraciji, dok je izoramnetin bio prisutan u najmanjoj. Antioksidacijski potencijal nativnog propolisa u in vitro uvjetima je bio relativno nizak. Međutim, propolis značajno povisuje antioksidacijski učinak in vivo uvjetima u jetri, plućima i mozgu miševa. Učinak nativnog propolisa pokazao ovisio je o dozi i to tako da je u manjoj dozi djelovao antioksidacijski (zaštitno), a u većoj dozi prooksidacijski (štetno). Oksidacijski status nakon obradaa nativnim propolisom nije pokazao tkivnu, ali je pokazao doznu ovisnost. Antioksidacijski status pokazao je tkivnu i doznu ovisnost ; u mozgu nije pokazao promjenu, dok je najveća promjena zabilježena u plućima i u manjoj mjeri u jetri. Promjena aktivnosti antioksidacijskih enzima u jetri nije korelirala s količinom njihove mRNA, dok je u plućima promjena u aktivnosti istih uglavnom bila proporcionalna promjeni u mRNA. Nije zapažena značajna promjena u ekpresiji proteina za sve ispitivane antioksidacijske enzime, niti obzirom na dozu, niti obzirom na ispitivano tkivo. Analizom DNA čipova utvrđeno je da propolis u dozi od 100 mg kg-1 u jetri ima zaštitni učinak, dok je u dozi od 300 mg kg-1 taj učinak prooksidacijski. U plućima je propolis u obje doze imao zaštitni učinak, dok u mozgu nije imao učinka na ispitivane gene. U hiperbaričkim uvjetima propolis je smanjio oksidacijski stres u sva tri ispitivana tkiva u dozi od 100 mg kg-1. U plućima je taj učinak propolis ostvario povećanjem aktivnosti antioksidacijskih enzima (MnSOD, KAT). Antioksidacijski učinak propolisa porijeklom iz Hrvatske do sada nije istraživan u in vivo sistemima. Isto tako po prvi puta se ispituje nativni propolis (tehnologijska inovacija) za razliku od do sada ispitivanih vodenih ili alkoholnih ekstrakata. Rezultati ove studije također pokazuju da sposobnost zaštitnog odgovora u plućima na oksidacijski stres koji postoji u novorođenih, ali se gubi u odraslih jedinki, može biti obnovljena uporabom nativnog propolisa tijekom hiperoksije. Ta spoznaja može pomoći u zaštiti od hiperoksije u populaciji odraslih tijekom terapije kisikom."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|57a035e5b1ae::15786c1f0f2930ea867a234fbcb8ef08","instance":[{"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2006-01-01"},"hostedby":{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"},"instancetype":{"classid":"doctoral thesis","classname":"doctoral 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b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigExploreTest.java @@ -0,0 +1,126 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.IOException; +import java.net.URI; + +import org.apache.commons.io.IOUtils; +import org.apache.solr.client.solrj.SolrQuery; +import org.apache.solr.client.solrj.response.QueryResponse; +import org.apache.solr.common.SolrDocument; +import org.apache.solr.common.params.CommonParams; +import org.apache.spark.SparkConf; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument; +import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class SolrConfigExploreTest extends SolrExploreTest { + + protected static SparkSession spark; + + private static final Integer batchSize = 100; + + @Mock + private ISLookUpService isLookUpService; + + @Mock + private ISLookupClient isLookupClient; + + @BeforeEach + public void prepareMocks() throws ISLookUpException, IOException { + isLookupClient.setIsLookup(isLookUpService); + + int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort(); + + Mockito + .when(isLookupClient.getDsId(Mockito.anyString())) + .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); + Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort)); + Mockito + .when(isLookupClient.getLayoutSource(Mockito.anyString())) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); + Mockito + .when(isLookupClient.getLayoutTransformer()) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); + } + + @BeforeAll + public static void before() { + + SparkConf conf = new SparkConf(); + conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); + conf.registerKryoClasses(new Class[] { + SerializableSolrInputDocument.class + }); + + conf.setMaster("local[1]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString()); + + spark = SparkSession + .builder() + .appName(XmlIndexingJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + + } + + @AfterAll + public static void tearDown() { + spark.stop(); + } + + @Test + public void testSolrConfig() throws Exception { + + String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; + + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null) + .run(isLookupClient); + Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); + + String[] queryStrings = { + "cancer", + "graph", + "graphs" + }; + + for (String q : queryStrings) { + SolrQuery query = new SolrQuery(); + query.setRequestHandler("/exploreSearch"); + query.add(CommonParams.Q, q); + query.set("debugQuery", "on"); + + log.info("Submit query to Solr with params: {}", query.toString()); + QueryResponse rsp = miniCluster.getSolrClient().query(query); +// System.out.println(rsp.getHighlighting()); +// System.out.println(rsp.getExplainMap()); + + for (SolrDocument doc : rsp.getResults()) { + System.out + .println( + doc.get("score") + "\t" + + doc.get("__indexrecordidentifier") + "\t" + + doc.get("resultidentifier") + "\t" + + doc.get("resultauthor") + "\t" + + doc.get("resultacceptanceyear") + "\t" + + doc.get("resultsubject") + "\t" + + doc.get("resulttitle") + "\t" + + doc.get("relprojectname") + "\t" + + doc.get("resultdescription") + "\t" + + doc.get("__all") + "\t"); + } + } + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java new file mode 100644 index 000000000..ab98b1da2 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrConfigTest.java @@ -0,0 +1,131 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.IOException; +import java.io.StringReader; +import java.net.URI; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.solr.client.solrj.SolrQuery; +import org.apache.solr.client.solrj.response.QueryResponse; +import org.apache.solr.common.SolrDocument; +import org.apache.solr.common.SolrInputField; +import org.apache.solr.common.params.CommonParams; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaPairRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.dom4j.io.SAXReader; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mock; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; + +import eu.dnetlib.dhp.oa.provision.model.SerializableSolrInputDocument; +import eu.dnetlib.dhp.oa.provision.utils.ISLookupClient; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpException; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +@ExtendWith(MockitoExtension.class) +public class SolrConfigTest extends SolrTest { + + protected static SparkSession spark; + + private static final Integer batchSize = 100; + + @Mock + private ISLookUpService isLookUpService; + + @Mock + private ISLookupClient isLookupClient; + + @BeforeEach + public void prepareMocks() throws ISLookUpException, IOException { + isLookupClient.setIsLookup(isLookUpService); + + int solrPort = URI.create("http://" + miniCluster.getZkClient().getZkServerAddress()).getPort(); + + Mockito + .when(isLookupClient.getDsId(Mockito.anyString())) + .thenReturn("313f0381-23b6-466f-a0b8-c72a9679ac4b_SW5kZXhEU1Jlc291cmNlcy9JbmRleERTUmVzb3VyY2VUeXBl"); + Mockito.when(isLookupClient.getZkHost()).thenReturn(String.format("127.0.0.1:%s/solr", solrPort)); + Mockito + .when(isLookupClient.getLayoutSource(Mockito.anyString())) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("fields.xml"))); + Mockito + .when(isLookupClient.getLayoutTransformer()) + .thenReturn(IOUtils.toString(getClass().getResourceAsStream("layoutToRecordTransformer.xsl"))); + } + + @BeforeAll + public static void before() { + + SparkConf conf = new SparkConf(); + conf.setAppName(XmlIndexingJobTest.class.getSimpleName()); + conf.registerKryoClasses(new Class[] { + SerializableSolrInputDocument.class + }); + + conf.setMaster("local[1]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.resolve("spark").toString()); + + spark = SparkSession + .builder() + .appName(XmlIndexingJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + + } + + @AfterAll + public static void tearDown() { + spark.stop(); + } + + @Test + public void testSolrConfig() throws Exception { + + String inputPath = "src/test/resources/eu/dnetlib/dhp/oa/provision/xml"; + + new XmlIndexingJob(spark, inputPath, FORMAT, batchSize, XmlIndexingJob.OutputFormat.SOLR, null) + .run(isLookupClient); + Assertions.assertEquals(0, miniCluster.getSolrClient().commit().getStatus()); + + String[] queryStrings = { + "cancer", + "graph", + "graphs" + }; + + for (String q : queryStrings) { + SolrQuery query = new SolrQuery(); + query.add(CommonParams.Q, q); + + log.info("Submit query to Solr with params: {}", query.toString()); + QueryResponse rsp = miniCluster.getSolrClient().query(query); + + for (SolrDocument doc : rsp.getResults()) { + System.out + .println( + doc.get("score") + "\t" + + doc.get("__indexrecordidentifier") + "\t" + + doc.get("resultidentifier") + "\t" + + doc.get("resultauthor") + "\t" + + doc.get("resultacceptanceyear") + "\t" + + doc.get("resultsubject") + "\t" + + doc.get("resulttitle") + "\t" + + doc.get("relprojectname") + "\t" + + doc.get("resultdescription") + "\t" + + doc.get("__all") + "\t"); + } + } + } +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java new file mode 100644 index 000000000..34a9465a7 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/SolrExploreTest.java @@ -0,0 +1,109 @@ + +package eu.dnetlib.dhp.oa.provision; + +import java.io.File; +import java.nio.file.Path; + +import org.apache.commons.io.FileUtils; +import org.apache.solr.client.solrj.embedded.JettyConfig; +import org.apache.solr.client.solrj.impl.CloudSolrClient; +import org.apache.solr.client.solrj.request.CollectionAdminRequest; +import org.apache.solr.client.solrj.request.ConfigSetAdminRequest; +import org.apache.solr.client.solrj.request.QueryRequest; +import org.apache.solr.cloud.MiniSolrCloudCluster; +import org.apache.solr.common.params.CollectionParams; +import org.apache.solr.common.params.CoreAdminParams; +import org.apache.solr.common.params.ModifiableSolrParams; +import org.apache.solr.common.util.NamedList; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.io.TempDir; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +public abstract class SolrExploreTest { + + protected static final Logger log = LoggerFactory.getLogger(SolrTest.class); + + protected static final String FORMAT = "test"; + protected static final String DEFAULT_COLLECTION = FORMAT + "-index-openaire"; + protected static final String CONFIG_NAME = "testConfig"; + + protected static MiniSolrCloudCluster miniCluster; + + @TempDir + public static Path workingDir; + + @BeforeAll + public static void setup() throws Exception { + + // random unassigned HTTP port + final int jettyPort = 0; + final JettyConfig jettyConfig = JettyConfig.builder().setPort(jettyPort).build(); + + log.info(String.format("working directory: %s", workingDir.toString())); + System.setProperty("solr.log.dir", workingDir.resolve("logs").toString()); + + // create a MiniSolrCloudCluster instance + miniCluster = new MiniSolrCloudCluster(2, workingDir.resolve("solr"), jettyConfig); + + // Upload Solr configuration directory to ZooKeeper + String solrZKConfigDir = "src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig"; + File configDir = new File(solrZKConfigDir); + + miniCluster.uploadConfigSet(configDir.toPath(), CONFIG_NAME); + + // override settings in the solrconfig include + System.setProperty("solr.tests.maxBufferedDocs", "100000"); + System.setProperty("solr.tests.maxIndexingThreads", "-1"); + System.setProperty("solr.tests.ramBufferSizeMB", "100"); + + // use non-test classes so RandomizedRunner isn't necessary + System.setProperty("solr.tests.mergeScheduler", "org.apache.lucene.index.ConcurrentMergeScheduler"); + System.setProperty("solr.directoryFactory", "solr.RAMDirectoryFactory"); + System.setProperty("solr.lock.type", "single"); + + log.info(new ConfigSetAdminRequest.List().process(miniCluster.getSolrClient()).toString()); + log + .info( + CollectionAdminRequest.ClusterStatus + .getClusterStatus() + .process(miniCluster.getSolrClient()) + .toString()); + + NamedList res = createCollection( + miniCluster.getSolrClient(), DEFAULT_COLLECTION, 4, 2, 20, CONFIG_NAME); + res.forEach(o -> log.info(o.toString())); + + miniCluster.getSolrClient().setDefaultCollection(DEFAULT_COLLECTION); + + log + .info( + CollectionAdminRequest.ClusterStatus + .getClusterStatus() + .process(miniCluster.getSolrClient()) + .toString()); + + } + + @AfterAll + public static void shutDown() throws Exception { + miniCluster.shutdown(); + FileUtils.deleteDirectory(workingDir.toFile()); + } + + protected static NamedList createCollection(CloudSolrClient client, String name, int numShards, + int replicationFactor, int maxShardsPerNode, String configName) throws Exception { + ModifiableSolrParams modParams = new ModifiableSolrParams(); + modParams.set(CoreAdminParams.ACTION, CollectionParams.CollectionAction.CREATE.name()); + modParams.set("name", name); + modParams.set("numShards", numShards); + modParams.set("replicationFactor", replicationFactor); + modParams.set("collection.configName", configName); + modParams.set("maxShardsPerNode", maxShardsPerNode); + QueryRequest request = new QueryRequest(modParams); + request.setPath("/admin/collections"); + return client.request(request); + } + +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/elevate.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/elevate.xml new file mode 100644 index 000000000..668332b28 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/elevate.xml @@ -0,0 +1,31 @@ +Unless required by applicable law or agreed to in writing, software + distributed under the License is distributed on an "AS IS" BASIS, + WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. + See the License for the specific language governing permissions and + limitations under the License. + --> + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ca.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ca.txt new file mode 100644 index 000000000..307a85f91 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ca.txt @@ -0,0 +1,8 @@ +# Set of Catalan contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +d +l +m +n +s +t diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_fr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_fr.txt new file mode 100644 index 000000000..f1bba51b2 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_fr.txt @@ -0,0 +1,15 @@ +# Set of French contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +l +m +t +qu +n +s +j +d +c +jusqu +quoiqu +lorsqu +puisqu diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ga.txt new file mode 100644 index 000000000..9ebe7fa34 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_ga.txt @@ -0,0 +1,5 @@ +# Set of Irish contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +d +m +b diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_it.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_it.txt new file mode 100644 index 000000000..cac040953 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/contractions_it.txt @@ -0,0 +1,23 @@ +# Set of Italian contractions for ElisionFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +c +l +all +dall +dell +nell +sull +coll +pell +gl +agl +dagl +degl +negl +sugl +un +m +t +s +v +d diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/hyphenations_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/hyphenations_ga.txt new file mode 100644 index 000000000..4d2642cc5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/hyphenations_ga.txt @@ -0,0 +1,5 @@ +# Set of Irish hyphenations for StopFilter +# TODO: load this as a resource from the analyzer and sync it in build.xml +h +n +t diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stemdict_nl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stemdict_nl.txt new file mode 100644 index 000000000..441072971 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stemdict_nl.txt @@ -0,0 +1,6 @@ +# Set of overrides for the dutch stemmer +# TODO: load this as a resource from the analyzer and sync it in build.xml +fiets fiets +bromfiets bromfiets +ei eier +kind kinder diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stoptags_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stoptags_ja.txt new file mode 100644 index 000000000..71b750845 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stoptags_ja.txt @@ -0,0 +1,420 @@ +# +# This file defines a Japanese stoptag set for JapanesePartOfSpeechStopFilter. +# +# Any token with a part-of-speech tag that exactly matches those defined in this +# file are removed from the token stream. +# +# Set your own stoptags by uncommenting the lines below. Note that comments are +# not allowed on the same line as a stoptag. See LUCENE-3745 for frequency lists, +# etc. that can be useful for building you own stoptag set. +# +# The entire possible tagset is provided below for convenience. +# +##### +# noun: unclassified nouns +#名詞 +# +# noun-common: Common nouns or nouns where the sub-classification is undefined +#名詞-一般 +# +# noun-proper: Proper nouns where the sub-classification is undefined +#名詞-固有名詞 +# +# noun-proper-misc: miscellaneous proper nouns +#名詞-固有名詞-一般 +# +# noun-proper-person: Personal names where the sub-classification is undefined +#名詞-固有名詞-人名 +# +# noun-proper-person-misc: names that cannot be divided into surname and +# given name; foreign names; names where the surname or given name is unknown. +# e.g. お市の方 +#名詞-固有名詞-人名-一般 +# +# noun-proper-person-surname: Mainly Japanese surnames. +# e.g. 山田 +#名詞-固有名詞-人名-姓 +# +# noun-proper-person-given_name: Mainly Japanese given names. +# e.g. 太郎 +#名詞-固有名詞-人名-名 +# +# noun-proper-organization: Names representing organizations. +# e.g. 通産省, NHK +#名詞-固有名詞-組織 +# +# noun-proper-place: Place names where the sub-classification is undefined +#名詞-固有名詞-地域 +# +# noun-proper-place-misc: Place names excluding countries. +# e.g. アジア, バルセロナ, 京都 +#名詞-固有名詞-地域-一般 +# +# noun-proper-place-country: Country names. +# e.g. 日本, オーストラリア +#名詞-固有名詞-地域-国 +# +# noun-pronoun: Pronouns where the sub-classification is undefined +#名詞-代名詞 +# +# noun-pronoun-misc: miscellaneous pronouns: +# e.g. それ, ここ, あいつ, あなた, あちこち, いくつ, どこか, なに, みなさん, みんな, わたくし, われわれ +#名詞-代名詞-一般 +# +# noun-pronoun-contraction: Spoken language contraction made by combining a +# pronoun and the particle 'wa'. +# e.g. ありゃ, こりゃ, こりゃあ, そりゃ, そりゃあ +#名詞-代名詞-縮約 +# +# noun-adverbial: Temporal nouns such as names of days or months that behave +# like adverbs. Nouns that represent amount or ratios and can be used adverbially, +# e.g. 金曜, 一月, 午後, 少量 +#名詞-副詞可能 +# +# noun-verbal: Nouns that take arguments with case and can appear followed by +# 'suru' and related verbs (する, できる, なさる, くださる) +# e.g. インプット, 愛着, 悪化, 悪戦苦闘, 一安心, 下取り +#名詞-サ変接続 +# +# noun-adjective-base: The base form of adjectives, words that appear before な ("na") +# e.g. 健康, 安易, 駄目, だめ +#名詞-形容動詞語幹 +# +# noun-numeric: Arabic numbers, Chinese numerals, and counters like 何 (回), 数. +# e.g. 0, 1, 2, 何, 数, 幾 +#名詞-数 +# +# noun-affix: noun affixes where the sub-classification is undefined +#名詞-非自立 +# +# noun-affix-misc: Of adnominalizers, the case-marker の ("no"), and words that +# attach to the base form of inflectional words, words that cannot be classified +# into any of the other categories below. This category includes indefinite nouns. +# e.g. あかつき, 暁, かい, 甲斐, 気, きらい, 嫌い, くせ, 癖, こと, 事, ごと, 毎, しだい, 次第, +# 順, せい, 所為, ついで, 序で, つもり, 積もり, 点, どころ, の, はず, 筈, はずみ, 弾み, +# 拍子, ふう, ふり, 振り, ほう, 方, 旨, もの, 物, 者, ゆえ, 故, ゆえん, 所以, わけ, 訳, +# わり, 割り, 割, ん-口語/, もん-口語/ +#名詞-非自立-一般 +# +# noun-affix-adverbial: noun affixes that that can behave as adverbs. +# e.g. あいだ, 間, あげく, 挙げ句, あと, 後, 余り, 以外, 以降, 以後, 以上, 以前, 一方, うえ, +# 上, うち, 内, おり, 折り, かぎり, 限り, きり, っきり, 結果, ころ, 頃, さい, 際, 最中, さなか, +# 最中, じたい, 自体, たび, 度, ため, 為, つど, 都度, とおり, 通り, とき, 時, ところ, 所, +# とたん, 途端, なか, 中, のち, 後, ばあい, 場合, 日, ぶん, 分, ほか, 他, まえ, 前, まま, +# 儘, 侭, みぎり, 矢先 +#名詞-非自立-副詞可能 +# +# noun-affix-aux: noun affixes treated as 助動詞 ("auxiliary verb") in school grammars +# with the stem よう(だ) ("you(da)"). +# e.g. よう, やう, 様 (よう) +#名詞-非自立-助動詞語幹 +# +# noun-affix-adjective-base: noun affixes that can connect to the indeclinable +# connection form な (aux "da"). +# e.g. みたい, ふう +#名詞-非自立-形容動詞語幹 +# +# noun-special: special nouns where the sub-classification is undefined. +#名詞-特殊 +# +# noun-special-aux: The そうだ ("souda") stem form that is used for reporting news, is +# treated as 助動詞 ("auxiliary verb") in school grammars, and attach to the base +# form of inflectional words. +# e.g. そう +#名詞-特殊-助動詞語幹 +# +# noun-suffix: noun suffixes where the sub-classification is undefined. +#名詞-接尾 +# +# noun-suffix-misc: Of the nouns or stem forms of other parts of speech that connect +# to ガル or タイ and can combine into compound nouns, words that cannot be classified into +# any of the other categories below. In general, this category is more inclusive than +# 接尾語 ("suffix") and is usually the last element in a compound noun. +# e.g. おき, かた, 方, 甲斐 (がい), がかり, ぎみ, 気味, ぐるみ, (～した) さ, 次第, 済 (ず) み, +# よう, (でき)っこ, 感, 観, 性, 学, 類, 面, 用 +#名詞-接尾-一般 +# +# noun-suffix-person: Suffixes that form nouns and attach to person names more often +# than other nouns. +# e.g. 君, 様, 著 +#名詞-接尾-人名 +# +# noun-suffix-place: Suffixes that form nouns and attach to place names more often +# than other nouns. +# e.g. 町, 市, 県 +#名詞-接尾-地域 +# +# noun-suffix-verbal: Of the suffixes that attach to nouns and form nouns, those that +# can appear before スル ("suru"). +# e.g. 化, 視, 分け, 入り, 落ち, 買い +#名詞-接尾-サ変接続 +# +# noun-suffix-aux: The stem form of そうだ (様態) that is used to indicate conditions, +# is treated as 助動詞 ("auxiliary verb") in school grammars, and attach to the +# conjunctive form of inflectional words. +# e.g. そう +#名詞-接尾-助動詞語幹 +# +# noun-suffix-adjective-base: Suffixes that attach to other nouns or the conjunctive +# form of inflectional words and appear before the copula だ ("da"). +# e.g. 的, げ, がち +#名詞-接尾-形容動詞語幹 +# +# noun-suffix-adverbial: Suffixes that attach to other nouns and can behave as adverbs. +# e.g. 後 (ご), 以後, 以降, 以前, 前後, 中, 末, 上, 時 (じ) +#名詞-接尾-副詞可能 +# +# noun-suffix-classifier: Suffixes that attach to numbers and form nouns. This category +# is more inclusive than 助数詞 ("classifier") and includes common nouns that attach +# to numbers. +# e.g. 個, つ, 本, 冊, パーセント, cm, kg, カ月, か国, 区画, 時間, 時半 +#名詞-接尾-助数詞 +# +# noun-suffix-special: Special suffixes that mainly attach to inflecting words. +# e.g. (楽し) さ, (考え) 方 +#名詞-接尾-特殊 +# +# noun-suffix-conjunctive: Nouns that behave like conjunctions and join two words +# together. +# e.g. (日本) 対 (アメリカ), 対 (アメリカ), (3) 対 (5), (女優) 兼 (主婦) +#名詞-接続詞的 +# +# noun-verbal_aux: Nouns that attach to the conjunctive particle て ("te") and are +# semantically verb-like. +# e.g. ごらん, ご覧, 御覧, 頂戴 +#名詞-動詞非自立的 +# +# noun-quotation: text that cannot be segmented into words, proverbs, Chinese poetry, +# dialects, English, etc. Currently, the only entry for 名詞 引用文字列 ("noun quotation") +# is いわく ("iwaku"). +#名詞-引用文字列 +# +# noun-nai_adjective: Words that appear before the auxiliary verb ない ("nai") and +# behave like an adjective. +# e.g. 申し訳, 仕方, とんでも, 違い +#名詞-ナイ形容詞語幹 +# +##### +# prefix: unclassified prefixes +#接頭詞 +# +# prefix-nominal: Prefixes that attach to nouns (including adjective stem forms) +# excluding numerical expressions. +# e.g. お (水), 某 (氏), 同 (社), 故 (～氏), 高 (品質), お (見事), ご (立派) +#接頭詞-名詞接続 +# +# prefix-verbal: Prefixes that attach to the imperative form of a verb or a verb +# in conjunctive form followed by なる/なさる/くださる. +# e.g. お (読みなさい), お (座り) +#接頭詞-動詞接続 +# +# prefix-adjectival: Prefixes that attach to adjectives. +# e.g. お (寒いですねえ), バカ (でかい) +#接頭詞-形容詞接続 +# +# prefix-numerical: Prefixes that attach to numerical expressions. +# e.g. 約, およそ, 毎時 +#接頭詞-数接続 +# +##### +# verb: unclassified verbs +#動詞 +# +# verb-main: +#動詞-自立 +# +# verb-auxiliary: +#動詞-非自立 +# +# verb-suffix: +#動詞-接尾 +# +##### +# adjective: unclassified adjectives +#形容詞 +# +# adjective-main: +#形容詞-自立 +# +# adjective-auxiliary: +#形容詞-非自立 +# +# adjective-suffix: +#形容詞-接尾 +# +##### +# adverb: unclassified adverbs +#副詞 +# +# adverb-misc: Words that can be segmented into one unit and where adnominal +# modification is not possible. +# e.g. あいかわらず, 多分 +#副詞-一般 +# +# adverb-particle_conjunction: Adverbs that can be followed by の, は, に, +# な, する, だ, etc. +# e.g. こんなに, そんなに, あんなに, なにか, なんでも +#副詞-助詞類接続 +# +##### +# adnominal: Words that only have noun-modifying forms. +# e.g. この, その, あの, どの, いわゆる, なんらかの, 何らかの, いろんな, こういう, そういう, ああいう, +# どういう, こんな, そんな, あんな, どんな, 大きな, 小さな, おかしな, ほんの, たいした, +# 「(, も) さる (ことながら)」, 微々たる, 堂々たる, 単なる, いかなる, 我が」「同じ, 亡き +#連体詞 +# +##### +# conjunction: Conjunctions that can occur independently. +# e.g. が, けれども, そして, じゃあ, それどころか +接続詞 +# +##### +# particle: unclassified particles. +助詞 +# +# particle-case: case particles where the subclassification is undefined. +助詞-格助詞 +# +# particle-case-misc: Case particles. +# e.g. から, が, で, と, に, へ, より, を, の, にて +助詞-格助詞-一般 +# +# particle-case-quote: the "to" that appears after nouns, a person’s speech, +# quotation marks, expressions of decisions from a meeting, reasons, judgements, +# conjectures, etc. +# e.g. ( だ) と (述べた.), ( である) と (して執行猶予...) +助詞-格助詞-引用 +# +# particle-case-compound: Compounds of particles and verbs that mainly behave +# like case particles. +# e.g. という, といった, とかいう, として, とともに, と共に, でもって, にあたって, に当たって, に当って, +# にあたり, に当たり, に当り, に当たる, にあたる, において, に於いて,に於て, における, に於ける, +# にかけ, にかけて, にかんし, に関し, にかんして, に関して, にかんする, に関する, に際し, +# に際して, にしたがい, に従い, に従う, にしたがって, に従って, にたいし, に対し, にたいして, +# に対して, にたいする, に対する, について, につき, につけ, につけて, につれ, につれて, にとって, +# にとり, にまつわる, によって, に依って, に因って, により, に依り, に因り, による, に依る, に因る, +# にわたって, にわたる, をもって, を以って, を通じ, を通じて, を通して, をめぐって, をめぐり, をめぐる, +# って-口語/, ちゅう-関西弁「という」/, (何) ていう (人)-口語/, っていう-口語/, といふ, とかいふ +助詞-格助詞-連語 +# +# particle-conjunctive: +# e.g. から, からには, が, けれど, けれども, けど, し, つつ, て, で, と, ところが, どころか, とも, ども, +# ながら, なり, ので, のに, ば, ものの, や ( した), やいなや, (ころん) じゃ(いけない)-口語/, +# (行っ) ちゃ(いけない)-口語/, (言っ) たって (しかたがない)-口語/, (それがなく)ったって (平気)-口語/ +助詞-接続助詞 +# +# particle-dependency: +# e.g. こそ, さえ, しか, すら, は, も, ぞ +助詞-係助詞 +# +# particle-adverbial: +# e.g. がてら, かも, くらい, 位, ぐらい, しも, (学校) じゃ(これが流行っている)-口語/, +# (それ)じゃあ (よくない)-口語/, ずつ, (私) なぞ, など, (私) なり (に), (先生) なんか (大嫌い)-口語/, +# (私) なんぞ, (先生) なんて (大嫌い)-口語/, のみ, だけ, (私) だって-口語/, だに, +# (彼)ったら-口語/, (お茶) でも (いかが), 等 (とう), (今後) とも, ばかり, ばっか-口語/, ばっかり-口語/, +# ほど, 程, まで, 迄, (誰) も (が)([助詞-格助詞] および [助詞-係助詞] の前に位置する「も」) +助詞-副助詞 +# +# particle-interjective: particles with interjective grammatical roles. +# e.g. (松島) や +助詞-間投助詞 +# +# particle-coordinate: +# e.g. と, たり, だの, だり, とか, なり, や, やら +助詞-並立助詞 +# +# particle-final: +# e.g. かい, かしら, さ, ぜ, (だ)っけ-口語/, (とまってる) で-方言/, な, ナ, なあ-口語/, ぞ, ね, ネ, +# ねぇ-口語/, ねえ-口語/, ねん-方言/, の, のう-口語/, や, よ, ヨ, よぉ-口語/, わ, わい-口語/ +助詞-終助詞 +# +# particle-adverbial/conjunctive/final: The particle "ka" when unknown whether it is +# adverbial, conjunctive, or sentence final. For example: +# (a) 「A か B か」. Ex:「(国内で運用する) か,(海外で運用する) か (.)」 +# (b) Inside an adverb phrase. Ex:「(幸いという) か (, 死者はいなかった.)」 +# 「(祈りが届いたせい) か (, 試験に合格した.)」 +# (c) 「かのように」. Ex:「(何もなかった) か (のように振る舞った.)」 +# e.g. か +助詞-副助詞／並立助詞／終助詞 +# +# particle-adnominalizer: The "no" that attaches to nouns and modifies +# non-inflectional words. +助詞-連体化 +# +# particle-adnominalizer: The "ni" and "to" that appear following nouns and adverbs +# that are giongo, giseigo, or gitaigo. +# e.g. に, と +助詞-副詞化 +# +# particle-special: A particle that does not fit into one of the above classifications. +# This includes particles that are used in Tanka, Haiku, and other poetry. +# e.g. かな, けむ, ( しただろう) に, (あんた) にゃ(わからん), (俺) ん (家) +助詞-特殊 +# +##### +# auxiliary-verb: +助動詞 +# +##### +# interjection: Greetings and other exclamations. +# e.g. おはよう, おはようございます, こんにちは, こんばんは, ありがとう, どうもありがとう, ありがとうございます, +# いただきます, ごちそうさま, さよなら, さようなら, はい, いいえ, ごめん, ごめんなさい +#感動詞 +# +##### +# symbol: unclassified Symbols. +記号 +# +# symbol-misc: A general symbol not in one of the categories below. +# e.g. [○◎@$〒→+] +記号-一般 +# +# symbol-comma: Commas +# e.g. [,、] +記号-読点 +# +# symbol-period: Periods and full stops. +# e.g. [.．。] +記号-句点 +# +# symbol-space: Full-width whitespace. +記号-空白 +# +# symbol-open_bracket: +# e.g. [({‘“『【] +記号-括弧開 +# +# symbol-close_bracket: +# e.g. [)}’”』」】] +記号-括弧閉 +# +# symbol-alphabetic: +#記号-アルファベット +# +##### +# other: unclassified other +#その他 +# +# other-interjection: Words that are hard to classify as noun-suffixes or +# sentence-final particles. +# e.g. (だ)ァ +その他-間投 +# +##### +# filler: Aizuchi that occurs during a conversation or sounds inserted as filler. +# e.g. あの, うんと, えと +フィラー +# +##### +# non-verbal: non-verbal sound. +非言語音 +# +##### +# fragment: +#語断片 +# +##### +# unknown: unknown part of speech. +#未知語 +# +##### End of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ar.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ar.txt new file mode 100644 index 000000000..046829db6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ar.txt @@ -0,0 +1,125 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +# Cleaned on October 11, 2009 (not normalized, so use before normalization) +# This means that when modifying this list, you might need to add some +# redundant entries, for example containing forms with both أ and ا +من +ومن +منها +منه +في +وفي +فيها +فيه +و +ف +ثم +او +أو +ب +بها +به +ا +أ +اى +اي +أي +أى +لا +ولا +الا +ألا +إلا +لكن +ما +وما +كما +فما +عن +مع +اذا +إذا +ان +أن +إن +انها +أنها +إنها +انه +أنه +إنه +بان +بأن +فان +فأن +وان +وأن +وإن +التى +التي +الذى +الذي +الذين +الى +الي +إلى +إلي +على +عليها +عليه +اما +أما +إما +ايضا +أيضا +كل +وكل +لم +ولم +لن +ولن +هى +هي +هو +وهى +وهي +وهو +فهى +فهي +فهو +انت +أنت +لك +لها +له +هذه +هذا +تلك +ذلك +هناك +كانت +كان +يكون +تكون +وكانت +وكان +غير +بعض +قد +نحو +بين +بينما +منذ +ضمن +حيث +الان +الآن +خلال +بعد +قبل +حتى +عند +عندما +لدى +جميع diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_bg.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_bg.txt new file mode 100644 index 000000000..1ae4ba2ae --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_bg.txt @@ -0,0 +1,193 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +а +аз +ако +ала +бе +без +беше +би +бил +била +били +било +близо +бъдат +бъде +бяха +в +вас +ваш +ваша +вероятно +вече +взема +ви +вие +винаги +все +всеки +всички +всичко +всяка +във +въпреки +върху +г +ги +главно +го +д +да +дали +до +докато +докога +дори +досега +доста +е +едва +един +ето +за +зад +заедно +заради +засега +затова +защо +защото +и +из +или +им +има +имат +иска +й +каза +как +каква +какво +както +какъв +като +кога +когато +което +които +кой +който +колко +която +къде +където +към +ли +м +ме +между +мен +ми +мнозина +мога +могат +може +моля +момента +му +н +на +над +назад +най +направи +напред +например +нас +не +него +нея +ни +ние +никой +нито +но +някои +някой +няма +обаче +около +освен +особено +от +отгоре +отново +още +пак +по +повече +повечето +под +поне +поради +после +почти +прави +пред +преди +през +при +пък +първо +с +са +само +се +сега +си +скоро +след +сме +според +сред +срещу +сте +съм +със +също +т +тази +така +такива +такъв +там +твой +те +тези +ти +тн +то +това +тогава +този +той +толкова +точно +трябва +тук +тъй +тя +тях +у +харесва +ч +че +често +чрез +ще +щом +я diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ca.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ca.txt new file mode 100644 index 000000000..3da65deaf --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ca.txt @@ -0,0 +1,220 @@ +# Catalan stopwords from http://github.com/vcl/cue.language (Apache 2 Licensed) +a +abans +ací +ah +així +això +al +als +aleshores +algun +alguna +algunes +alguns +alhora +allà +allí +allò +altra +altre +altres +amb +ambdós +ambdues +apa +aquell +aquella +aquelles +aquells +aquest +aquesta +aquestes +aquests +aquí +baix +cada +cadascú +cadascuna +cadascunes +cadascuns +com +contra +d'un +d'una +d'unes +d'uns +dalt +de +del +dels +des +després +dins +dintre +donat +doncs +durant +e +eh +el +els +em +en +encara +ens +entre +érem +eren +éreu +es +és +esta +està +estàvem +estaven +estàveu +esteu +et +etc +ets +fins +fora +gairebé +ha +han +has +havia +he +hem +heu +hi +ho +i +igual +iguals +ja +l'hi +la +les +li +li'n +llavors +m'he +ma +mal +malgrat +mateix +mateixa +mateixes +mateixos +me +mentre +més +meu +meus +meva +meves +molt +molta +moltes +molts +mon +mons +n'he +n'hi +ne +ni +no +nogensmenys +només +nosaltres +nostra +nostre +nostres +o +oh +oi +on +pas +pel +pels +per +però +perquè +poc +poca +pocs +poques +potser +propi +qual +quals +quan +quant +que +què +quelcom +qui +quin +quina +quines +quins +s'ha +s'han +sa +semblant +semblants +ses +seu +seus +seva +seva +seves +si +sobre +sobretot +sóc +solament +sols +son +són +sons +sota +sou +t'ha +t'han +t'he +ta +tal +també +tampoc +tan +tant +tanta +tantes +teu +teus +teva +teves +ton +tons +tot +tota +totes +tots +un +una +unes +uns +us +va +vaig +vam +van +vas +veu +vosaltres +vostra +vostre +vostres diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_cz.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_cz.txt new file mode 100644 index 000000000..53c6097da --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_cz.txt @@ -0,0 +1,172 @@ +a +s +k +o +i +u +v +z +dnes +cz +tímto +budeš +budem +byli +jseš +můj +svým +ta +tomto +tohle +tuto +tyto +jej +zda +proč +máte +tato +kam +tohoto +kdo +kteří +mi +nám +tom +tomuto +mít +nic +proto +kterou +byla +toho +protože +asi +ho +naši +napište +re +což +tím +takže +svých +její +svými +jste +aj +tu +tedy +teto +bylo +kde +ke +pravé +ji +nad +nejsou +či +pod +téma +mezi +přes +ty +pak +vám +ani +když +však +neg +jsem +tento +článku +články +aby +jsme +před +pta +jejich +byl +ještě +až +bez +také +pouze +první +vaše +která +nás +nový +tipy +pokud +může +strana +jeho +své +jiné +zprávy +nové +není +vás +jen +podle +zde +už +být +více +bude +již +než +který +by +které +co +nebo +ten +tak +má +při +od +po +jsou +jak +další +ale +si +se +ve +to +jako +za +zpět +ze +do +pro +je +na +atd +atp +jakmile +přičemž +já +on +ona +ono +oni +ony +my +vy +jí +ji +mě +mne +jemu +tomu +těm +těmu +němu +němuž +jehož +jíž +jelikož +jež +jakož +načež diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_da.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_da.txt new file mode 100644 index 000000000..42e6145b9 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_da.txt @@ -0,0 +1,110 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/danish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Danish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + +og | and +i | in +jeg | I +det | that (dem. pronoun)/it (pers. pronoun) +at | that (in front of a sentence)/to (with infinitive) +en | a/an +den | it (pers. pronoun)/that (dem. pronoun) +til | to/at/for/until/against/by/of/into, more +er | present tense of "to be" +som | who, as +på | on/upon/in/on/at/to/after/of/with/for, on +de | they +med | with/by/in, along +han | he +af | of/by/from/off/for/in/with/on, off +for | at/for/to/from/by/of/ago, in front/before, because +ikke | not +der | who/which, there/those +var | past tense of "to be" +mig | me/myself +sig | oneself/himself/herself/itself/themselves +men | but +et | a/an/one, one (number), someone/somebody/one +har | present tense of "to have" +om | round/about/for/in/a, about/around/down, if +vi | we +min | my +havde | past tense of "to have" +ham | him +hun | she +nu | now +over | over/above/across/by/beyond/past/on/about, over/past +da | then, when/as/since +fra | from/off/since, off, since +du | you +ud | out +sin | his/her/its/one's +dem | them +os | us/ourselves +op | up +man | you/one +hans | his +hvor | where +eller | or +hvad | what +skal | must/shall etc. +selv | myself/youself/herself/ourselves etc., even +her | here +alle | all/everyone/everybody etc. +vil | will (verb) +blev | past tense of "to stay/to remain/to get/to become" +kunne | could +ind | in +når | when +være | present tense of "to be" +dog | however/yet/after all +noget | something +ville | would +jo | you know/you see (adv), yes +deres | their/theirs +efter | after/behind/according to/for/by/from, later/afterwards +ned | down +skulle | should +denne | this +end | than +dette | this +mit | my/mine +også | also +under | under/beneath/below/during, below/underneath +have | have +dig | you +anden | other +hende | her +mine | my +alt | everything +meget | much/very, plenty of +sit | his, her, its, one's +sine | his, her, its, one's +vor | our +mod | against +disse | these +hvis | if +din | your/yours +nogle | some +hos | by/at +blive | be/become +mange | many +ad | by/through +bliver | present tense of "to be/to become" +hendes | her/hers +været | be +thi | for (conj) +jer | you +sådan | such, like this/like that diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_de.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_de.txt new file mode 100644 index 000000000..86525e7ae --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_de.txt @@ -0,0 +1,294 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/german/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A German stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | The number of forms in this list is reduced significantly by passing it + | through the German stemmer. + + +aber | but + +alle | all +allem +allen +aller +alles + +als | than, as +also | so +am | an + dem +an | at + +ander | other +andere +anderem +anderen +anderer +anderes +anderm +andern +anderr +anders + +auch | also +auf | on +aus | out of +bei | by +bin | am +bis | until +bist | art +da | there +damit | with it +dann | then + +der | the +den +des +dem +die +das + +daß | that + +derselbe | the same +derselben +denselben +desselben +demselben +dieselbe +dieselben +dasselbe + +dazu | to that + +dein | thy +deine +deinem +deinen +deiner +deines + +denn | because + +derer | of those +dessen | of him + +dich | thee +dir | to thee +du | thou + +dies | this +diese +diesem +diesen +dieser +dieses + + +doch | (several meanings) +dort | (over) there + + +durch | through + +ein | a +eine +einem +einen +einer +eines + +einig | some +einige +einigem +einigen +einiger +einiges + +einmal | once + +er | he +ihn | him +ihm | to him + +es | it +etwas | something + +euer | your +eure +eurem +euren +eurer +eures + +für | for +gegen | towards +gewesen | p.p. of sein +hab | have +habe | have +haben | have +hat | has +hatte | had +hatten | had +hier | here +hin | there +hinter | behind + +ich | I +mich | me +mir | to me + + +ihr | you, to her +ihre +ihrem +ihren +ihrer +ihres +euch | to you + +im | in + dem +in | in +indem | while +ins | in + das +ist | is + +jede | each, every +jedem +jeden +jeder +jedes + +jene | that +jenem +jenen +jener +jenes + +jetzt | now +kann | can + +kein | no +keine +keinem +keinen +keiner +keines + +können | can +könnte | could +machen | do +man | one + +manche | some, many a +manchem +manchen +mancher +manches + +mein | my +meine +meinem +meinen +meiner +meines + +mit | with +muss | must +musste | had to +nach | to(wards) +nicht | not +nichts | nothing +noch | still, yet +nun | now +nur | only +ob | whether +oder | or +ohne | without +sehr | very + +sein | his +seine +seinem +seinen +seiner +seines + +selbst | self +sich | herself + +sie | they, she +ihnen | to them + +sind | are +so | so + +solche | such +solchem +solchen +solcher +solches + +soll | shall +sollte | should +sondern | but +sonst | else +über | over +um | about, around +und | and + +uns | us +unse +unsem +unsen +unser +unses + +unter | under +viel | much +vom | von + dem +von | from +vor | before +während | while +war | was +waren | were +warst | wast +was | what +weg | away, off +weil | because +weiter | further + +welche | which +welchem +welchen +welcher +welches + +wenn | when +werde | will +werden | will +wie | how +wieder | again +will | want +wir | we +wird | will +wirst | willst +wo | where +wollen | want +wollte | wanted +würde | would +würden | would +zu | to +zum | zu + dem +zur | zu + der +zwar | indeed +zwischen | between + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_el.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_el.txt new file mode 100644 index 000000000..232681f5b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_el.txt @@ -0,0 +1,78 @@ +# Lucene Greek Stopwords list +# Note: by default this file is used after GreekLowerCaseFilter, +# so when modifying this file use 'σ' instead of 'ς' +ο +η +το +οι +τα +του +τησ +των +τον +την +και +κι +κ +ειμαι +εισαι +ειναι +ειμαστε +ειστε +στο +στον +στη +στην +μα +αλλα +απο +για +προσ +με +σε +ωσ +παρα +αντι +κατα +μετα +θα +να +δε +δεν +μη +μην +επι +ενω +εαν +αν +τοτε +που +πωσ +ποιοσ +ποια +ποιο +ποιοι +ποιεσ +ποιων +ποιουσ +αυτοσ +αυτη +αυτο +αυτοι +αυτων +αυτουσ +αυτεσ +αυτα +εκεινοσ +εκεινη +εκεινο +εκεινοι +εκεινεσ +εκεινα +εκεινων +εκεινουσ +οπωσ +ομωσ +ισωσ +οσο +οτι diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_en.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_en.txt new file mode 100644 index 000000000..2c164c0b2 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_en.txt @@ -0,0 +1,54 @@ +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +# a couple of test stopwords to test that the words are really being +# configured from this file: +stopworda +stopwordb + +# Standard english stop words taken from Lucene's StopAnalyzer +a +an +and +are +as +at +be +but +by +for +if +in +into +is +it +no +not +of +on +or +such +that +the +their +then +there +these +they +this +to +was +will +with diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_es.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_es.txt new file mode 100644 index 000000000..487d78c8d --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_es.txt @@ -0,0 +1,356 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/spanish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Spanish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + + | The following is a ranked list (commonest to rarest) of stopwords + | deriving from a large sample of text. + + | Extra words have been added at the end. + +de | from, of +la | the, her +que | who, that +el | the +en | in +y | and +a | to +los | the, them +del | de + el +se | himself, from him etc +las | the, them +por | for, by, etc +un | a +para | for +con | with +no | no +una | a +su | his, her +al | a + el + | es from SER +lo | him +como | how +más | more +pero | pero +sus | su plural +le | to him, her +ya | already +o | or + | fue from SER +este | this + | ha from HABER +sí | himself etc +porque | because +esta | this + | son from SER +entre | between + | está from ESTAR +cuando | when +muy | very +sin | without +sobre | on + | ser from SER + | tiene from TENER +también | also +me | me +hasta | until +hay | there is/are +donde | where + | han from HABER +quien | whom, that + | están from ESTAR + | estado from ESTAR +desde | from +todo | all +nos | us +durante | during + | estados from ESTAR +todos | all +uno | a +les | to them +ni | nor +contra | against +otros | other + | fueron from SER +ese | that +eso | that + | había from HABER +ante | before +ellos | they +e | and (variant of y) +esto | this +mí | me +antes | before +algunos | some +qué | what? +unos | a +yo | I +otro | other +otras | other +otra | other +él | he +tanto | so much, many +esa | that +estos | these +mucho | much, many +quienes | who +nada | nothing +muchos | many +cual | who + | sea from SER +poco | few +ella | she +estar | to be + | haber from HABER +estas | these + | estaba from ESTAR + | estamos from ESTAR +algunas | some +algo | something +nosotros | we + + | other forms + +mi | me +mis | mi plural +tú | thou +te | thee +ti | thee +tu | thy +tus | tu plural +ellas | they +nosotras | we +vosotros | you +vosotras | you +os | you +mío | mine +mía | +míos | +mías | +tuyo | thine +tuya | +tuyos | +tuyas | +suyo | his, hers, theirs +suya | +suyos | +suyas | +nuestro | ours +nuestra | +nuestros | +nuestras | +vuestro | yours +vuestra | +vuestros | +vuestras | +esos | those +esas | those + + | forms of estar, to be (not including the infinitive): +estoy +estás +está +estamos +estáis +están +esté +estés +estemos +estéis +estén +estaré +estarás +estará +estaremos +estaréis +estarán +estaría +estarías +estaríamos +estaríais +estarían +estaba +estabas +estábamos +estabais +estaban +estuve +estuviste +estuvo +estuvimos +estuvisteis +estuvieron +estuviera +estuvieras +estuviéramos +estuvierais +estuvieran +estuviese +estuvieses +estuviésemos +estuvieseis +estuviesen +estando +estado +estada +estados +estadas +estad + + | forms of haber, to have (not including the infinitive): +he +has +ha +hemos +habéis +han +haya +hayas +hayamos +hayáis +hayan +habré +habrás +habrá +habremos +habréis +habrán +habría +habrías +habríamos +habríais +habrían +había +habías +habíamos +habíais +habían +hube +hubiste +hubo +hubimos +hubisteis +hubieron +hubiera +hubieras +hubiéramos +hubierais +hubieran +hubiese +hubieses +hubiésemos +hubieseis +hubiesen +habiendo +habido +habida +habidos +habidas + + | forms of ser, to be (not including the infinitive): +soy +eres +es +somos +sois +son +sea +seas +seamos +seáis +sean +seré +serás +será +seremos +seréis +serán +sería +serías +seríamos +seríais +serían +era +eras +éramos +erais +eran +fui +fuiste +fue +fuimos +fuisteis +fueron +fuera +fueras +fuéramos +fuerais +fueran +fuese +fueses +fuésemos +fueseis +fuesen +siendo +sido + | sed also means 'thirst' + + | forms of tener, to have (not including the infinitive): +tengo +tienes +tiene +tenemos +tenéis +tienen +tenga +tengas +tengamos +tengáis +tengan +tendré +tendrás +tendrá +tendremos +tendréis +tendrán +tendría +tendrías +tendríamos +tendríais +tendrían +tenía +tenías +teníamos +teníais +tenían +tuve +tuviste +tuvo +tuvimos +tuvisteis +tuvieron +tuviera +tuvieras +tuviéramos +tuvierais +tuvieran +tuviese +tuvieses +tuviésemos +tuvieseis +tuviesen +teniendo +tenido +tenida +tenidos +tenidas +tened + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_eu.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_eu.txt new file mode 100644 index 000000000..25f1db934 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_eu.txt @@ -0,0 +1,99 @@ +# example set of basque stopwords +al +anitz +arabera +asko +baina +bat +batean +batek +bati +batzuei +batzuek +batzuetan +batzuk +bera +beraiek +berau +berauek +bere +berori +beroriek +beste +bezala +da +dago +dira +ditu +du +dute +edo +egin +ere +eta +eurak +ez +gainera +gu +gutxi +guzti +haiei +haiek +haietan +hainbeste +hala +han +handik +hango +hara +hari +hark +hartan +hau +hauei +hauek +hauetan +hemen +hemendik +hemengo +hi +hona +honek +honela +honetan +honi +hor +hori +horiei +horiek +horietan +horko +horra +horrek +horrela +horretan +horri +hortik +hura +izan +ni +noiz +nola +non +nondik +nongo +nor +nora +ze +zein +zen +zenbait +zenbat +zer +zergatik +ziren +zituen +zu +zuek +zuen +zuten diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fa.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fa.txt new file mode 100644 index 000000000..723641c6d --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fa.txt @@ -0,0 +1,313 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +# Note: by default this file is used after normalization, so when adding entries +# to this file, use the arabic 'ي' instead of 'ی' +انان +نداشته +سراسر +خياه +ايشان +وي +تاكنون +بيشتري +دوم +پس +ناشي +وگو +يا +داشتند +سپس +هنگام +هرگز +پنج +نشان +امسال +ديگر +گروهي +شدند +چطور +ده +و +دو +نخستين +ولي +چرا +چه +وسط +ه +كدام +قابل +يك +رفت +هفت +همچنين +در +هزار +بله +بلي +شايد +اما +شناسي +گرفته +دهد +داشته +دانست +داشتن +خواهيم +ميليارد +وقتيكه +امد +خواهد +جز +اورده +شده +بلكه +خدمات +شدن +برخي +نبود +بسياري +جلوگيري +حق +كردند +نوعي +بعري +نكرده +نظير +نبايد +بوده +بودن +داد +اورد +هست +جايي +شود +دنبال +داده +بايد +سابق +هيچ +همان +انجا +كمتر +كجاست +گردد +كسي +تر +مردم +تان +دادن +بودند +سري +جدا +ندارند +مگر +يكديگر +دارد +دهند +بنابراين +هنگامي +سمت +جا +انچه +خود +دادند +زياد +دارند +اثر +بدون +بهترين +بيشتر +البته +به +براساس +بيرون +كرد +بعضي +گرفت +توي +اي +ميليون +او +جريان +تول +بر +مانند +برابر +باشيم +مدتي +گويند +اكنون +تا +تنها +جديد +چند +بي +نشده +كردن +كردم +گويد +كرده +كنيم +نمي +نزد +روي +قصد +فقط +بالاي +ديگران +اين +ديروز +توسط +سوم +ايم +دانند +سوي +استفاده +شما +كنار +داريم +ساخته +طور +امده +رفته +نخست +بيست +نزديك +طي +كنيد +از +انها +تمامي +داشت +يكي +طريق +اش +چيست +روب +نمايد +گفت +چندين +چيزي +تواند +ام +ايا +با +ان +ايد +ترين +اينكه +ديگري +راه +هايي +بروز +همچنان +پاعين +كس +حدود +مختلف +مقابل +چيز +گيرد +ندارد +ضد +همچون +سازي +شان +مورد +باره +مرسي +خويش +برخوردار +چون +خارج +شش +هنوز +تحت +ضمن +هستيم +گفته +فكر +بسيار +پيش +براي +روزهاي +انكه +نخواهد +بالا +كل +وقتي +كي +چنين +كه +گيري +نيست +است +كجا +كند +نيز +يابد +بندي +حتي +توانند +عقب +خواست +كنند +بين +تمام +همه +ما +باشند +مثل +شد +اري +باشد +اره +طبق +بعد +اگر +صورت +غير +جاي +بيش +ريزي +اند +زيرا +چگونه +بار +لطفا +مي +درباره +من +ديده +همين +گذاري +برداري +علت +گذاشته +هم +فوق +نه +ها +شوند +اباد +همواره +هر +اول +خواهند +چهار +نام +امروز +مان +هاي +قبل +كنم +سعي +تازه +را +هستند +زير +جلوي +عنوان +بود diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fi.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fi.txt new file mode 100644 index 000000000..4372c9a05 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fi.txt @@ -0,0 +1,97 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/finnish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + +| forms of BE + +olla +olen +olet +on +olemme +olette +ovat +ole | negative form + +oli +olisi +olisit +olisin +olisimme +olisitte +olisivat +olit +olin +olimme +olitte +olivat +ollut +olleet + +en | negation +et +ei +emme +ette +eivät + +|Nom Gen Acc Part Iness Elat Illat Adess Ablat Allat Ess Trans +minä minun minut minua minussa minusta minuun minulla minulta minulle | I +sinä sinun sinut sinua sinussa sinusta sinuun sinulla sinulta sinulle | you +hän hänen hänet häntä hänessä hänestä häneen hänellä häneltä hänelle | he she +me meidän meidät meitä meissä meistä meihin meillä meiltä meille | we +te teidän teidät teitä teissä teistä teihin teillä teiltä teille | you +he heidän heidät heitä heissä heistä heihin heillä heiltä heille | they + +tämä tämän tätä tässä tästä tähän tallä tältä tälle tänä täksi | this +tuo tuon tuotä tuossa tuosta tuohon tuolla tuolta tuolle tuona tuoksi | that +se sen sitä siinä siitä siihen sillä siltä sille sinä siksi | it +nämä näiden näitä näissä näistä näihin näillä näiltä näille näinä näiksi | these +nuo noiden noita noissa noista noihin noilla noilta noille noina noiksi | those +ne niiden niitä niissä niistä niihin niillä niiltä niille niinä niiksi | they + +kuka kenen kenet ketä kenessä kenestä keneen kenellä keneltä kenelle kenenä keneksi| who +ketkä keiden ketkä keitä keissä keistä keihin keillä keiltä keille keinä keiksi | (pl) +mikä minkä minkä mitä missä mistä mihin millä miltä mille minä miksi | which what +mitkä | (pl) + +joka jonka jota jossa josta johon jolla jolta jolle jona joksi | who which +jotka joiden joita joissa joista joihin joilla joilta joille joina joiksi | (pl) + +| conjunctions + +että | that +ja | and +jos | if +koska | because +kuin | than +mutta | but +niin | so +sekä | and +sillä | for +tai | or +vaan | but +vai | or +vaikka | although + + +| prepositions + +kanssa | with +mukaan | according to +noin | about +poikki | across +yli | over, across + +| other + +kun | when +niin | so +nyt | now +itse | self + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fr.txt new file mode 100644 index 000000000..749abae68 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_fr.txt @@ -0,0 +1,186 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/french/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A French stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + +au | a + le +aux | a + les +avec | with +ce | this +ces | these +dans | with +de | of +des | de + les +du | de + le +elle | she +en | `of them' etc +et | and +eux | them +il | he +je | I +la | the +le | the +leur | their +lui | him +ma | my (fem) +mais | but +me | me +même | same; as in moi-même (myself) etc +mes | me (pl) +moi | me +mon | my (masc) +ne | not +nos | our (pl) +notre | our +nous | we +on | one +ou | where +par | by +pas | not +pour | for +qu | que before vowel +que | that +qui | who +sa | his, her (fem) +se | oneself +ses | his (pl) +son | his, her (masc) +sur | on +ta | thy (fem) +te | thee +tes | thy (pl) +toi | thee +ton | thy (masc) +tu | thou +un | a +une | a +vos | your (pl) +votre | your +vous | you + + | single letter forms + +c | c' +d | d' +j | j' +l | l' +à | to, at +m | m' +n | n' +s | s' +t | t' +y | there + + | forms of être (not including the infinitive): +été +étée +étées +étés +étant +suis +es +est +sommes +êtes +sont +serai +seras +sera +serons +serez +seront +serais +serait +serions +seriez +seraient +étais +était +étions +étiez +étaient +fus +fut +fûmes +fûtes +furent +sois +soit +soyons +soyez +soient +fusse +fusses +fût +fussions +fussiez +fussent + + | forms of avoir (not including the infinitive): +ayant +eu +eue +eues +eus +ai +as +avons +avez +ont +aurai +auras +aura +aurons +aurez +auront +aurais +aurait +aurions +auriez +auraient +avais +avait +avions +aviez +avaient +eut +eûmes +eûtes +eurent +aie +aies +ait +ayons +ayez +aient +eusse +eusses +eût +eussions +eussiez +eussent + + | Later additions (from Jean-Christophe Deschamps) +ceci | this +cela | that +celà | that +cet | this +cette | this +ici | here +ils | they +les | the (pl) +leurs | their (pl) +quel | which +quels | which +quelle | which +quelles | which +sans | without +soi | oneself + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ga.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ga.txt new file mode 100644 index 000000000..9ff88d747 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ga.txt @@ -0,0 +1,110 @@ + +a +ach +ag +agus +an +aon +ar +arna +as +b' +ba +beirt +bhúr +caoga +ceathair +ceathrar +chomh +chtó +chuig +chun +cois +céad +cúig +cúigear +d' +daichead +dar +de +deich +deichniúr +den +dhá +do +don +dtí +dá +dár +dó +faoi +faoin +faoina +faoinár +fara +fiche +gach +gan +go +gur +haon +hocht +i +iad +idir +in +ina +ins +inár +is +le +leis +lena +lenár +m' +mar +mo +mé +na +nach +naoi +naonúr +ná +ní +níor +nó +nócha +ocht +ochtar +os +roimh +sa +seacht +seachtar +seachtó +seasca +seisear +siad +sibh +sinn +sna +sé +sí +tar +thar +thú +triúr +trí +trína +trínár +tríocha +tú +um +ár +é +éis +í +ó +ón +óna +ónár diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_gl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_gl.txt new file mode 100644 index 000000000..d8760b12c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_gl.txt @@ -0,0 +1,161 @@ +# galican stopwords +a +aínda +alí +aquel +aquela +aquelas +aqueles +aquilo +aquí +ao +aos +as +así +á +ben +cando +che +co +coa +comigo +con +connosco +contigo +convosco +coas +cos +cun +cuns +cunha +cunhas +da +dalgunha +dalgunhas +dalgún +dalgúns +das +de +del +dela +delas +deles +desde +deste +do +dos +dun +duns +dunha +dunhas +e +el +ela +elas +eles +en +era +eran +esa +esas +ese +eses +esta +estar +estaba +está +están +este +estes +estiven +estou +eu +é +facer +foi +foron +fun +había +hai +iso +isto +la +las +lle +lles +lo +los +mais +me +meu +meus +min +miña +miñas +moi +na +nas +neste +nin +no +non +nos +nosa +nosas +noso +nosos +nós +nun +nunha +nuns +nunhas +o +os +ou +ó +ós +para +pero +pode +pois +pola +polas +polo +polos +por +que +se +senón +ser +seu +seus +sexa +sido +sobre +súa +súas +tamén +tan +te +ten +teñen +teño +ter +teu +teus +ti +tido +tiña +tiven +túa +túas +un +unha +unhas +uns +vos +vosa +vosas +voso +vosos +vós diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hi.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hi.txt new file mode 100644 index 000000000..86286bb08 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hi.txt @@ -0,0 +1,235 @@ +# Also see http://www.opensource.org/licenses/bsd-license.html +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# This file was created by Jacques Savoy and is distributed under the BSD license. +# Note: by default this file also contains forms normalized by HindiNormalizer +# for spelling variation (see section below), such that it can be used whether or +# not you enable that feature. When adding additional entries to this list, +# please add the normalized form as well. +अंदर +अत +अपना +अपनी +अपने +अभी +आदि +आप +इत्यादि +इन +इनका +इन्हीं +इन्हें +इन्हों +इस +इसका +इसकी +इसके +इसमें +इसी +इसे +उन +उनका +उनकी +उनके +उनको +उन्हीं +उन्हें +उन्हों +उस +उसके +उसी +उसे +एक +एवं +एस +ऐसे +और +कई +कर +करता +करते +करना +करने +करें +कहते +कहा +का +काफ़ी +कि +कितना +किन्हें +किन्हों +किया +किर +किस +किसी +किसे +की +कुछ +कुल +के +को +कोई +कौन +कौनसा +गया +घर +जब +जहाँ +जा +जितना +जिन +जिन्हें +जिन्हों +जिस +जिसे +जीधर +जैसा +जैसे +जो +तक +तब +तरह +तिन +तिन्हें +तिन्हों +तिस +तिसे +तो +था +थी +थे +दबारा +दिया +दुसरा +दूसरे +दो +द्वारा +न +नहीं +ना +निहायत +नीचे +ने +पर +पर +पहले +पूरा +पे +फिर +बनी +बही +बहुत +बाद +बाला +बिलकुल +भी +भीतर +मगर +मानो +मे +में +यदि +यह +यहाँ +यही +या +यिह +ये +रखें +रहा +रहे +ऱ्वासा +लिए +लिये +लेकिन +व +वर्ग +वह +वह +वहाँ +वहीं +वाले +वुह +वे +वग़ैरह +संग +सकता +सकते +सबसे +सभी +साथ +साबुत +साभ +सारा +से +सो +ही +हुआ +हुई +हुए +है +हैं +हो +होता +होती +होते +होना +होने +# additional normalized forms of the above +अपनि +जेसे +होति +सभि +तिंहों +इंहों +दवारा +इसि +किंहें +थि +उंहों +ओर +जिंहें +वहिं +अभि +बनि +हि +उंहिं +उंहें +हें +वगेरह +एसे +रवासा +कोन +निचे +काफि +उसि +पुरा +भितर +हे +बहि +वहां +कोइ +यहां +जिंहों +तिंहें +किसि +कइ +यहि +इंहिं +जिधर +इंहें +अदि +इतयादि +हुइ +कोनसा +इसकि +दुसरे +जहां +अप +किंहों +उनकि +भि +वरग +हुअ +जेसा +नहिं diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hu.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hu.txt new file mode 100644 index 000000000..37526da8a --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hu.txt @@ -0,0 +1,211 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/hungarian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + +| Hungarian stop word list +| prepared by Anna Tordai + +a +ahogy +ahol +aki +akik +akkor +alatt +által +általában +amely +amelyek +amelyekben +amelyeket +amelyet +amelynek +ami +amit +amolyan +amíg +amikor +át +abban +ahhoz +annak +arra +arról +az +azok +azon +azt +azzal +azért +aztán +azután +azonban +bár +be +belül +benne +cikk +cikkek +cikkeket +csak +de +e +eddig +egész +egy +egyes +egyetlen +egyéb +egyik +egyre +ekkor +el +elég +ellen +elő +először +előtt +első +én +éppen +ebben +ehhez +emilyen +ennek +erre +ez +ezt +ezek +ezen +ezzel +ezért +és +fel +felé +hanem +hiszen +hogy +hogyan +igen +így +illetve +ill. +ill +ilyen +ilyenkor +ison +ismét +itt +jó +jól +jobban +kell +kellett +keresztül +keressünk +ki +kívül +között +közül +legalább +lehet +lehetett +legyen +lenne +lenni +lesz +lett +maga +magát +majd +majd +már +más +másik +meg +még +mellett +mert +mely +melyek +mi +mit +míg +miért +milyen +mikor +minden +mindent +mindenki +mindig +mint +mintha +mivel +most +nagy +nagyobb +nagyon +ne +néha +nekem +neki +nem +néhány +nélkül +nincs +olyan +ott +össze +ő +ők +őket +pedig +persze +rá +s +saját +sem +semmi +sok +sokat +sokkal +számára +szemben +szerint +szinte +talán +tehát +teljes +tovább +továbbá +több +úgy +ugyanis +új +újabb +újra +után +utána +utolsó +vagy +vagyis +valaki +valami +valamint +való +vagyok +van +vannak +volt +voltam +voltak +voltunk +vissza +vele +viszont +volna diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hy.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hy.txt new file mode 100644 index 000000000..60c1c50fb --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_hy.txt @@ -0,0 +1,46 @@ +# example set of Armenian stopwords. +այդ +այլ +այն +այս +դու +դուք +եմ +են +ենք +ես +եք +է +էի +էին +էինք +էիր +էիք +էր +ըստ +թ +ի +ին +իսկ +իր +կամ +համար +հետ +հետո +մենք +մեջ +մի +ն +նա +նաև +նրա +նրանք +որ +որը +որոնք +որպես +ու +ում +պիտի +վրա +և diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_id.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_id.txt new file mode 100644 index 000000000..4617f83a5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_id.txt @@ -0,0 +1,359 @@ +# from appendix D of: A Study of Stemming Effects on Information +# Retrieval in Bahasa Indonesia +ada +adanya +adalah +adapun +agak +agaknya +agar +akan +akankah +akhirnya +aku +akulah +amat +amatlah +anda +andalah +antar +diantaranya +antara +antaranya +diantara +apa +apaan +mengapa +apabila +apakah +apalagi +apatah +atau +ataukah +ataupun +bagai +bagaikan +sebagai +sebagainya +bagaimana +bagaimanapun +sebagaimana +bagaimanakah +bagi +bahkan +bahwa +bahwasanya +sebaliknya +banyak +sebanyak +beberapa +seberapa +begini +beginian +beginikah +beginilah +sebegini +begitu +begitukah +begitulah +begitupun +sebegitu +belum +belumlah +sebelum +sebelumnya +sebenarnya +berapa +berapakah +berapalah +berapapun +betulkah +sebetulnya +biasa +biasanya +bila +bilakah +bisa +bisakah +sebisanya +boleh +bolehkah +bolehlah +buat +bukan +bukankah +bukanlah +bukannya +cuma +percuma +dahulu +dalam +dan +dapat +dari +daripada +dekat +demi +demikian +demikianlah +sedemikian +dengan +depan +di +dia +dialah +dini +diri +dirinya +terdiri +dong +dulu +enggak +enggaknya +entah +entahlah +terhadap +terhadapnya +hal +hampir +hanya +hanyalah +harus +haruslah +harusnya +seharusnya +hendak +hendaklah +hendaknya +hingga +sehingga +ia +ialah +ibarat +ingin +inginkah +inginkan +ini +inikah +inilah +itu +itukah +itulah +jangan +jangankan +janganlah +jika +jikalau +juga +justru +kala +kalau +kalaulah +kalaupun +kalian +kami +kamilah +kamu +kamulah +kan +kapan +kapankah +kapanpun +dikarenakan +karena +karenanya +ke +kecil +kemudian +kenapa +kepada +kepadanya +ketika +seketika +khususnya +kini +kinilah +kiranya +sekiranya +kita +kitalah +kok +lagi +lagian +selagi +lah +lain +lainnya +melainkan +selaku +lalu +melalui +terlalu +lama +lamanya +selama +selama +selamanya +lebih +terlebih +bermacam +macam +semacam +maka +makanya +makin +malah +malahan +mampu +mampukah +mana +manakala +manalagi +masih +masihkah +semasih +masing +mau +maupun +semaunya +memang +mereka +merekalah +meski +meskipun +semula +mungkin +mungkinkah +nah +namun +nanti +nantinya +nyaris +oleh +olehnya +seorang +seseorang +pada +padanya +padahal +paling +sepanjang +pantas +sepantasnya +sepantasnyalah +para +pasti +pastilah +per +pernah +pula +pun +merupakan +rupanya +serupa +saat +saatnya +sesaat +saja +sajalah +saling +bersama +sama +sesama +sambil +sampai +sana +sangat +sangatlah +saya +sayalah +se +sebab +sebabnya +sebuah +tersebut +tersebutlah +sedang +sedangkan +sedikit +sedikitnya +segala +segalanya +segera +sesegera +sejak +sejenak +sekali +sekalian +sekalipun +sesekali +sekaligus +sekarang +sekarang +sekitar +sekitarnya +sela +selain +selalu +seluruh +seluruhnya +semakin +sementara +sempat +semua +semuanya +sendiri +sendirinya +seolah +seperti +sepertinya +sering +seringnya +serta +siapa +siapakah +siapapun +disini +disinilah +sini +sinilah +sesuatu +sesuatunya +suatu +sesudah +sesudahnya +sudah +sudahkah +sudahlah +supaya +tadi +tadinya +tak +tanpa +setelah +telah +tentang +tentu +tentulah +tentunya +tertentu +seterusnya +tapi +tetapi +setiap +tiap +setidaknya +tidak +tidakkah +tidaklah +toh +waduh +wah +wahai +sewaktu +walau +walaupun +wong +yaitu +yakni +yang diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_it.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_it.txt new file mode 100644 index 000000000..1219cc773 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_it.txt @@ -0,0 +1,303 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/italian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | An Italian stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + +ad | a (to) before vowel +al | a + il +allo | a + lo +ai | a + i +agli | a + gli +all | a + l' +agl | a + gl' +alla | a + la +alle | a + le +con | with +col | con + il +coi | con + i (forms collo, cogli etc are now very rare) +da | from +dal | da + il +dallo | da + lo +dai | da + i +dagli | da + gli +dall | da + l' +dagl | da + gll' +dalla | da + la +dalle | da + le +di | of +del | di + il +dello | di + lo +dei | di + i +degli | di + gli +dell | di + l' +degl | di + gl' +della | di + la +delle | di + le +in | in +nel | in + el +nello | in + lo +nei | in + i +negli | in + gli +nell | in + l' +negl | in + gl' +nella | in + la +nelle | in + le +su | on +sul | su + il +sullo | su + lo +sui | su + i +sugli | su + gli +sull | su + l' +sugl | su + gl' +sulla | su + la +sulle | su + le +per | through, by +tra | among +contro | against +io | I +tu | thou +lui | he +lei | she +noi | we +voi | you +loro | they +mio | my +mia | +miei | +mie | +tuo | +tua | +tuoi | thy +tue | +suo | +sua | +suoi | his, her +sue | +nostro | our +nostra | +nostri | +nostre | +vostro | your +vostra | +vostri | +vostre | +mi | me +ti | thee +ci | us, there +vi | you, there +lo | him, the +la | her, the +li | them +le | them, the +gli | to him, the +ne | from there etc +il | the +un | a +uno | a +una | a +ma | but +ed | and +se | if +perché | why, because +anche | also +come | how +dov | where (as dov') +dove | where +che | who, that +chi | who +cui | whom +non | not +più | more +quale | who, that +quanto | how much +quanti | +quanta | +quante | +quello | that +quelli | +quella | +quelle | +questo | this +questi | +questa | +queste | +si | yes +tutto | all +tutti | all + + | single letter forms: + +a | at +c | as c' for ce or ci +e | and +i | the +l | as l' +o | or + + | forms of avere, to have (not including the infinitive): + +ho +hai +ha +abbiamo +avete +hanno +abbia +abbiate +abbiano +avrò +avrai +avrà +avremo +avrete +avranno +avrei +avresti +avrebbe +avremmo +avreste +avrebbero +avevo +avevi +aveva +avevamo +avevate +avevano +ebbi +avesti +ebbe +avemmo +aveste +ebbero +avessi +avesse +avessimo +avessero +avendo +avuto +avuta +avuti +avute + + | forms of essere, to be (not including the infinitive): +sono +sei +è +siamo +siete +sia +siate +siano +sarò +sarai +sarà +saremo +sarete +saranno +sarei +saresti +sarebbe +saremmo +sareste +sarebbero +ero +eri +era +eravamo +eravate +erano +fui +fosti +fu +fummo +foste +furono +fossi +fosse +fossimo +fossero +essendo + + | forms of fare, to do (not including the infinitive, fa, fat-): +faccio +fai +facciamo +fanno +faccia +facciate +facciano +farò +farai +farà +faremo +farete +faranno +farei +faresti +farebbe +faremmo +fareste +farebbero +facevo +facevi +faceva +facevamo +facevate +facevano +feci +facesti +fece +facemmo +faceste +fecero +facessi +facesse +facessimo +facessero +facendo + + | forms of stare, to be (not including the infinitive): +sto +stai +sta +stiamo +stanno +stia +stiate +stiano +starò +starai +starà +staremo +starete +staranno +starei +staresti +starebbe +staremmo +stareste +starebbero +stavo +stavi +stava +stavamo +stavate +stavano +stetti +stesti +stette +stemmo +steste +stettero +stessi +stesse +stessimo +stessero +stando diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ja.txt new file mode 100644 index 000000000..d4321be6b --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ja.txt @@ -0,0 +1,127 @@ +# +# This file defines a stopword set for Japanese. +# +# This set is made up of hand-picked frequent terms from segmented Japanese Wikipedia. +# Punctuation characters and frequent kanji have mostly been left out. See LUCENE-3745 +# for frequency lists, etc. that can be useful for making your own set (if desired) +# +# Note that there is an overlap between these stopwords and the terms stopped when used +# in combination with the JapanesePartOfSpeechStopFilter. When editing this file, note +# that comments are not allowed on the same line as stopwords. +# +# Also note that stopping is done in a case-insensitive manner. Change your StopFilter +# configuration if you need case-sensitive stopping. Lastly, note that stopping is done +# using the same character width as the entries in this file. Since this StopFilter is +# normally done after a CJKWidthFilter in your chain, you would usually want your romaji +# entries to be in half-width and your kana entries to be in full-width. +# +の +に +は +を +た +が +で +て +と +し +れ +さ +ある +いる +も +する +から +な +こと +として +い +や +れる +など +なっ +ない +この +ため +その +あっ +よう +また +もの +という +あり +まで +られ +なる +へ +か +だ +これ +によって +により +おり +より +による +ず +なり +られる +において +ば +なかっ +なく +しかし +について +せ +だっ +その後 +できる +それ +う +ので +なお +のみ +でき +き +つ +における +および +いう +さらに +でも +ら +たり +その他 +に関する +たち +ます +ん +なら +に対して +特に +せる +及び +これら +とき +では +にて +ほか +ながら +うち +そして +とともに +ただし +かつて +それぞれ +または +お +ほど +ものの +に対する +ほとんど +と共に +といった +です +とも +ところ +ここ +##### End of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_lv.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_lv.txt new file mode 100644 index 000000000..e21a23c06 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_lv.txt @@ -0,0 +1,172 @@ +# Set of Latvian stopwords from A Stemming Algorithm for Latvian, Karlis Kreslins +# the original list of over 800 forms was refined: +# pronouns, adverbs, interjections were removed +# +# prepositions +aiz +ap +ar +apakš +ārpus +augšpus +bez +caur +dēļ +gar +iekš +iz +kopš +labad +lejpus +līdz +no +otrpus +pa +par +pār +pēc +pie +pirms +pret +priekš +starp +šaipus +uz +viņpus +virs +virspus +zem +apakšpus +# Conjunctions +un +bet +jo +ja +ka +lai +tomēr +tikko +turpretī +arī +kaut +gan +tādēļ +tā +ne +tikvien +vien +kā +ir +te +vai +kamēr +# Particles +ar +diezin +droši +diemžēl +nebūt +ik +it +taču +nu +pat +tiklab +iekšpus +nedz +tik +nevis +turpretim +jeb +iekam +iekām +iekāms +kolīdz +līdzko +tiklīdz +jebšu +tālab +tāpēc +nekā +itin +jā +jau +jel +nē +nezin +tad +tikai +vis +tak +iekams +vien +# modal verbs +būt +biju +biji +bija +bijām +bijāt +esmu +esi +esam +esat +būšu +būsi +būs +būsim +būsiet +tikt +tiku +tiki +tika +tikām +tikāt +tieku +tiec +tiek +tiekam +tiekat +tikšu +tiks +tiksim +tiksiet +tapt +tapi +tapāt +topat +tapšu +tapsi +taps +tapsim +tapsiet +kļūt +kļuvu +kļuvi +kļuva +kļuvām +kļuvāt +kļūstu +kļūsti +kļūst +kļūstam +kļūstat +kļūšu +kļūsi +kļūs +kļūsim +kļūsiet +# verbs +varēt +varēju +varējām +varēšu +varēsim +var +varēji +varējāt +varēsi +varēsiet +varat +varēja +varēs diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_nl.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_nl.txt new file mode 100644 index 000000000..47a2aeacf --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_nl.txt @@ -0,0 +1,119 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/dutch/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Dutch stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large sample of Dutch text. + + | Dutch stop words frequently exhibit homonym clashes. These are indicated + | clearly below. + +de | the +en | and +van | of, from +ik | I, the ego +te | (1) chez, at etc, (2) to, (3) too +dat | that, which +die | that, those, who, which +in | in, inside +een | a, an, one +hij | he +het | the, it +niet | not, nothing, naught +zijn | (1) to be, being, (2) his, one's, its +is | is +was | (1) was, past tense of all persons sing. of 'zijn' (to be) (2) wax, (3) the washing, (4) rise of river +op | on, upon, at, in, up, used up +aan | on, upon, to (as dative) +met | with, by +als | like, such as, when +voor | (1) before, in front of, (2) furrow +had | had, past tense all persons sing. of 'hebben' (have) +er | there +maar | but, only +om | round, about, for etc +hem | him +dan | then +zou | should/would, past tense all persons sing. of 'zullen' +of | or, whether, if +wat | what, something, anything +mijn | possessive and noun 'mine' +men | people, 'one' +dit | this +zo | so, thus, in this way +door | through by +over | over, across +ze | she, her, they, them +zich | oneself +bij | (1) a bee, (2) by, near, at +ook | also, too +tot | till, until +je | you +mij | me +uit | out of, from +der | Old Dutch form of 'van der' still found in surnames +daar | (1) there, (2) because +haar | (1) her, their, them, (2) hair +naar | (1) unpleasant, unwell etc, (2) towards, (3) as +heb | present first person sing. of 'to have' +hoe | how, why +heeft | present third person sing. of 'to have' +hebben | 'to have' and various parts thereof +deze | this +u | you +want | (1) for, (2) mitten, (3) rigging +nog | yet, still +zal | 'shall', first and third person sing. of verb 'zullen' (will) +me | me +zij | she, they +nu | now +ge | 'thou', still used in Belgium and south Netherlands +geen | none +omdat | because +iets | something, somewhat +worden | to become, grow, get +toch | yet, still +al | all, every, each +waren | (1) 'were' (2) to wander, (3) wares, (3) +veel | much, many +meer | (1) more, (2) lake +doen | to do, to make +toen | then, when +moet | noun 'spot/mote' and present form of 'to must' +ben | (1) am, (2) 'are' in interrogative second person singular of 'to be' +zonder | without +kan | noun 'can' and present form of 'to be able' +hun | their, them +dus | so, consequently +alles | all, everything, anything +onder | under, beneath +ja | yes, of course +eens | once, one day +hier | here +wie | who +werd | imperfect third person sing. of 'become' +altijd | always +doch | yet, but etc +wordt | present third person sing. of 'become' +wezen | (1) to be, (2) 'been' as in 'been fishing', (3) orphans +kunnen | to be able +ons | us/our +zelf | self +tegen | against, towards, at +na | after, near +reeds | already +wil | (1) present tense of 'want', (2) 'will', noun, (3) fender +kon | could; past tense of 'to be able' +niets | nothing +uw | your +iemand | somebody +geweest | been; past participle of 'be' +andere | other diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_no.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_no.txt new file mode 100644 index 000000000..a7a2c28ba --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_no.txt @@ -0,0 +1,194 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/norwegian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Norwegian stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This stop word list is for the dominant bokmål dialect. Words unique + | to nynorsk are marked *. + + | Revised by Jan Bruusgaard , Jan 2005 + +og | and +i | in +jeg | I +det | it/this/that +at | to (w. inf.) +en | a/an +et | a/an +den | it/this/that +til | to +er | is/am/are +som | who/that +på | on +de | they / you(formal) +med | with +han | he +av | of +ikke | not +ikkje | not * +der | there +så | so +var | was/were +meg | me +seg | you +men | but +ett | one +har | have +om | about +vi | we +min | my +mitt | my +ha | have +hadde | had +hun | she +nå | now +over | over +da | when/as +ved | by/know +fra | from +du | you +ut | out +sin | your +dem | them +oss | us +opp | up +man | you/one +kan | can +hans | his +hvor | where +eller | or +hva | what +skal | shall/must +selv | self (reflective) +sjøl | self (reflective) +her | here +alle | all +vil | will +bli | become +ble | became +blei | became * +blitt | have become +kunne | could +inn | in +når | when +være | be +kom | come +noen | some +noe | some +ville | would +dere | you +som | who/which/that +deres | their/theirs +kun | only/just +ja | yes +etter | after +ned | down +skulle | should +denne | this +for | for/because +deg | you +si | hers/his +sine | hers/his +sitt | hers/his +mot | against +å | to +meget | much +hvorfor | why +dette | this +disse | these/those +uten | without +hvordan | how +ingen | none +din | your +ditt | your +blir | become +samme | same +hvilken | which +hvilke | which (plural) +sånn | such a +inni | inside/within +mellom | between +vår | our +hver | each +hvem | who +vors | us/ours +hvis | whose +både | both +bare | only/just +enn | than +fordi | as/because +før | before +mange | many +også | also +slik | just +vært | been +være | to be +båe | both * +begge | both +siden | since +dykk | your * +dykkar | yours * +dei | they * +deira | them * +deires | theirs * +deim | them * +di | your (fem.) * +då | as/when * +eg | I * +ein | a/an * +eit | a/an * +eitt | a/an * +elles | or * +honom | he * +hjå | at * +ho | she * +hoe | she * +henne | her +hennar | her/hers +hennes | hers +hoss | how * +hossen | how * +ikkje | not * +ingi | noone * +inkje | noone * +korleis | how * +korso | how * +kva | what/which * +kvar | where * +kvarhelst | where * +kven | who/whom * +kvi | why * +kvifor | why * +me | we * +medan | while * +mi | my * +mine | my * +mykje | much * +no | now * +nokon | some (masc./neut.) * +noka | some (fem.) * +nokor | some * +noko | some * +nokre | some * +si | his/hers * +sia | since * +sidan | since * +so | so * +somt | some * +somme | some * +um | about* +upp | up * +vere | be * +vore | was * +verte | become * +vort | become * +varte | became * +vart | became * + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_pt.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_pt.txt new file mode 100644 index 000000000..acfeb01af --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_pt.txt @@ -0,0 +1,253 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/portuguese/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Portuguese stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + + | The following is a ranked list (commonest to rarest) of stopwords + | deriving from a large sample of text. + + | Extra words have been added at the end. + +de | of, from +a | the; to, at; her +o | the; him +que | who, that +e | and +do | de + o +da | de + a +em | in +um | a +para | for + | é from SER +com | with +não | not, no +uma | a +os | the; them +no | em + o +se | himself etc +na | em + a +por | for +mais | more +as | the; them +dos | de + os +como | as, like +mas | but + | foi from SER +ao | a + o +ele | he +das | de + as + | tem from TER +à | a + a +seu | his +sua | her +ou | or + | ser from SER +quando | when +muito | much + | há from HAV +nos | em + os; us +já | already, now + | está from EST +eu | I +também | also +só | only, just +pelo | per + o +pela | per + a +até | up to +isso | that +ela | he +entre | between + | era from SER +depois | after +sem | without +mesmo | same +aos | a + os + | ter from TER +seus | his +quem | whom +nas | em + as +me | me +esse | that +eles | they + | estão from EST +você | you + | tinha from TER + | foram from SER +essa | that +num | em + um +nem | nor +suas | her +meu | my +às | a + as +minha | my + | têm from TER +numa | em + uma +pelos | per + os +elas | they + | havia from HAV + | seja from SER +qual | which + | será from SER +nós | we + | tenho from TER +lhe | to him, her +deles | of them +essas | those +esses | those +pelas | per + as +este | this + | fosse from SER +dele | of him + + | other words. There are many contractions such as naquele = em+aquele, + | mo = me+o, but they are rare. + | Indefinite article plural forms are also rare. + +tu | thou +te | thee +vocês | you (plural) +vos | you +lhes | to them +meus | my +minhas +teu | thy +tua +teus +tuas +nosso | our +nossa +nossos +nossas + +dela | of her +delas | of them + +esta | this +estes | these +estas | these +aquele | that +aquela | that +aqueles | those +aquelas | those +isto | this +aquilo | that + + | forms of estar, to be (not including the infinitive): +estou +está +estamos +estão +estive +esteve +estivemos +estiveram +estava +estávamos +estavam +estivera +estivéramos +esteja +estejamos +estejam +estivesse +estivéssemos +estivessem +estiver +estivermos +estiverem + + | forms of haver, to have (not including the infinitive): +hei +há +havemos +hão +houve +houvemos +houveram +houvera +houvéramos +haja +hajamos +hajam +houvesse +houvéssemos +houvessem +houver +houvermos +houverem +houverei +houverá +houveremos +houverão +houveria +houveríamos +houveriam + + | forms of ser, to be (not including the infinitive): +sou +somos +são +era +éramos +eram +fui +foi +fomos +foram +fora +fôramos +seja +sejamos +sejam +fosse +fôssemos +fossem +for +formos +forem +serei +será +seremos +serão +seria +seríamos +seriam + + | forms of ter, to have (not including the infinitive): +tenho +tem +temos +tém +tinha +tínhamos +tinham +tive +teve +tivemos +tiveram +tivera +tivéramos +tenha +tenhamos +tenham +tivesse +tivéssemos +tivessem +tiver +tivermos +tiverem +terei +terá +teremos +terão +teria +teríamos +teriam diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ro.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ro.txt new file mode 100644 index 000000000..4fdee90a5 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ro.txt @@ -0,0 +1,233 @@ +# This file was created by Jacques Savoy and is distributed under the BSD license. +# See http://members.unine.ch/jacques.savoy/clef/index.html. +# Also see http://www.opensource.org/licenses/bsd-license.html +acea +aceasta +această +aceea +acei +aceia +acel +acela +acele +acelea +acest +acesta +aceste +acestea +aceşti +aceştia +acolo +acum +ai +aia +aibă +aici +al +ăla +ale +alea +ălea +altceva +altcineva +am +ar +are +aş +aşadar +asemenea +asta +ăsta +astăzi +astea +ăstea +ăştia +asupra +aţi +au +avea +avem +aveţi +azi +bine +bucur +bună +ca +că +căci +când +care +cărei +căror +cărui +cât +câte +câţi +către +câtva +ce +cel +ceva +chiar +cînd +cine +cineva +cît +cîte +cîţi +cîtva +contra +cu +cum +cumva +curând +curînd +da +dă +dacă +dar +datorită +de +deci +deja +deoarece +departe +deşi +din +dinaintea +dintr +dintre +drept +după +ea +ei +el +ele +eram +este +eşti +eu +face +fără +fi +fie +fiecare +fii +fim +fiţi +iar +ieri +îi +îl +îmi +împotriva +în +înainte +înaintea +încât +încît +încotro +între +întrucât +întrucît +îţi +la +lângă +le +li +lîngă +lor +lui +mă +mâine +mea +mei +mele +mereu +meu +mi +mine +mult +multă +mulţi +ne +nicăieri +nici +nimeni +nişte +noastră +noastre +noi +noştri +nostru +nu +ori +oricând +oricare +oricât +orice +oricînd +oricine +oricît +oricum +oriunde +până +pe +pentru +peste +pînă +poate +pot +prea +prima +primul +prin +printr +sa +să +săi +sale +sau +său +se +şi +sînt +sîntem +sînteţi +spre +sub +sunt +suntem +sunteţi +ta +tăi +tale +tău +te +ţi +ţie +tine +toată +toate +tot +toţi +totuşi +tu +un +una +unde +undeva +unei +unele +uneori +unor +vă +vi +voastră +voastre +voi +voştri +vostru +vouă +vreo +vreun diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ru.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ru.txt new file mode 100644 index 000000000..55271400c --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_ru.txt @@ -0,0 +1,243 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/russian/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | a russian stop word list. comments begin with vertical bar. each stop + | word is at the start of a line. + + | this is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + | letter `ё' is translated to `е'. + +и | and +в | in/into +во | alternative form +не | not +что | what/that +он | he +на | on/onto +я | i +с | from +со | alternative form +как | how +а | milder form of `no' (but) +то | conjunction and form of `that' +все | all +она | she +так | so, thus +его | him +но | but +да | yes/and +ты | thou +к | towards, by +у | around, chez +же | intensifier particle +вы | you +за | beyond, behind +бы | conditional/subj. particle +по | up to, along +только | only +ее | her +мне | to me +было | it was +вот | here is/are, particle +от | away from +меня | me +еще | still, yet, more +нет | no, there isnt/arent +о | about +из | out of +ему | to him +теперь | now +когда | when +даже | even +ну | so, well +вдруг | suddenly +ли | interrogative particle +если | if +уже | already, but homonym of `narrower' +или | or +ни | neither +быть | to be +был | he was +него | prepositional form of его +до | up to +вас | you accusative +нибудь | indef. suffix preceded by hyphen +опять | again +уж | already, but homonym of `adder' +вам | to you +сказал | he said +ведь | particle `after all' +там | there +потом | then +себя | oneself +ничего | nothing +ей | to her +может | usually with `быть' as `maybe' +они | they +тут | here +где | where +есть | there is/are +надо | got to, must +ней | prepositional form of ей +для | for +мы | we +тебя | thee +их | them, their +чем | than +была | she was +сам | self +чтоб | in order to +без | without +будто | as if +человек | man, person, one +чего | genitive form of `what' +раз | once +тоже | also +себе | to oneself +под | beneath +жизнь | life +будет | will be +ж | short form of intensifer particle `же' +тогда | then +кто | who +этот | this +говорил | was saying +того | genitive form of `that' +потому | for that reason +этого | genitive form of `this' +какой | which +совсем | altogether +ним | prepositional form of `его', `они' +здесь | here +этом | prepositional form of `этот' +один | one +почти | almost +мой | my +тем | instrumental/dative plural of `тот', `то' +чтобы | full form of `in order that' +нее | her (acc.) +кажется | it seems +сейчас | now +были | they were +куда | where to +зачем | why +сказать | to say +всех | all (acc., gen. preposn. plural) +никогда | never +сегодня | today +можно | possible, one can +при | by +наконец | finally +два | two +об | alternative form of `о', about +другой | another +хоть | even +после | after +над | above +больше | more +тот | that one (masc.) +через | across, in +эти | these +нас | us +про | about +всего | in all, only, of all +них | prepositional form of `они' (they) +какая | which, feminine +много | lots +разве | interrogative particle +сказала | she said +три | three +эту | this, acc. fem. sing. +моя | my, feminine +впрочем | moreover, besides +хорошо | good +свою | ones own, acc. fem. sing. +этой | oblique form of `эта', fem. `this' +перед | in front of +иногда | sometimes +лучше | better +чуть | a little +том | preposn. form of `that one' +нельзя | one must not +такой | such a one +им | to them +более | more +всегда | always +конечно | of course +всю | acc. fem. sing of `all' +между | between + + + | b: some paradigms + | + | personal pronouns + | + | я меня мне мной [мною] + | ты тебя тебе тобой [тобою] + | он его ему им [него, нему, ним] + | она ее эи ею [нее, нэи, нею] + | оно его ему им [него, нему, ним] + | + | мы нас нам нами + | вы вас вам вами + | они их им ими [них, ним, ними] + | + | себя себе собой [собою] + | + | demonstrative pronouns: этот (this), тот (that) + | + | этот эта это эти + | этого эты это эти + | этого этой этого этих + | этому этой этому этим + | этим этой этим [этою] этими + | этом этой этом этих + | + | тот та то те + | того ту то те + | того той того тех + | тому той тому тем + | тем той тем [тою] теми + | том той том тех + | + | determinative pronouns + | + | (a) весь (all) + | + | весь вся все все + | всего всю все все + | всего всей всего всех + | всему всей всему всем + | всем всей всем [всею] всеми + | всем всей всем всех + | + | (b) сам (himself etc) + | + | сам сама само сами + | самого саму само самих + | самого самой самого самих + | самому самой самому самим + | самим самой самим [самою] самими + | самом самой самом самих + | + | stems of verbs `to be', `to have', `to do' and modal + | + | быть бы буд быв есть суть + | име + | дел + | мог мож мочь + | уме + | хоч хот + | долж + | можн + | нужн + | нельзя + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_sv.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_sv.txt new file mode 100644 index 000000000..096f87f67 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_sv.txt @@ -0,0 +1,133 @@ + | From svn.tartarus.org/snowball/trunk/website/algorithms/swedish/stop.txt + | This file is distributed under the BSD License. + | See http://snowball.tartarus.org/license.php + | Also see http://www.opensource.org/licenses/bsd-license.html + | - Encoding was converted to UTF-8. + | - This notice was added. + | + | NOTE: To use this file with StopFilterFactory, you must specify format="snowball" + + | A Swedish stop word list. Comments begin with vertical bar. Each stop + | word is at the start of a line. + + | This is a ranked list (commonest to rarest) of stopwords derived from + | a large text sample. + + | Swedish stop words occasionally exhibit homonym clashes. For example + | så = so, but also seed. These are indicated clearly below. + +och | and +det | it, this/that +att | to (with infinitive) +i | in, at +en | a +jag | I +hon | she +som | who, that +han | he +på | on +den | it, this/that +med | with +var | where, each +sig | him(self) etc +för | for +så | so (also: seed) +till | to +är | is +men | but +ett | a +om | if; around, about +hade | had +de | they, these/those +av | of +icke | not, no +mig | me +du | you +henne | her +då | then, when +sin | his +nu | now +har | have +inte | inte någon = no one +hans | his +honom | him +skulle | 'sake' +hennes | her +där | there +min | my +man | one (pronoun) +ej | nor +vid | at, by, on (also: vast) +kunde | could +något | some etc +från | from, off +ut | out +när | when +efter | after, behind +upp | up +vi | we +dem | them +vara | be +vad | what +över | over +än | than +dig | you +kan | can +sina | his +här | here +ha | have +mot | towards +alla | all +under | under (also: wonder) +någon | some etc +eller | or (else) +allt | all +mycket | much +sedan | since +ju | why +denna | this/that +själv | myself, yourself etc +detta | this/that +åt | to +utan | without +varit | was +hur | how +ingen | no +mitt | my +ni | you +bli | to be, become +blev | from bli +oss | us +din | thy +dessa | these/those +några | some etc +deras | their +blir | from bli +mina | my +samma | (the) same +vilken | who, that +er | you, your +sådan | such a +vår | our +blivit | from bli +dess | its +inom | within +mellan | between +sådant | such a +varför | why +varje | each +vilka | who, that +ditt | thy +vem | who +vilket | who, that +sitta | his +sådana | such a +vart | each +dina | thy +vars | whose +vårt | our +våra | our +ert | your +era | your +vilkas | whose + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_th.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_th.txt new file mode 100644 index 000000000..07f0fabe6 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_th.txt @@ -0,0 +1,119 @@ +# Thai stopwords from: +# "Opinion Detection in Thai Political News Columns +# Based on Subjectivity Analysis" +# Khampol Sukhum, Supot Nitsuwat, and Choochart Haruechaiyasak +ไว้ +ไม่ +ไป +ได้ +ให้ +ใน +โดย +แห่ง +แล้ว +และ +แรก +แบบ +แต่ +เอง +เห็น +เลย +เริ่ม +เรา +เมื่อ +เพื่อ +เพราะ +เป็นการ +เป็น +เปิดเผย +เปิด +เนื่องจาก +เดียวกัน +เดียว +เช่น +เฉพาะ +เคย +เข้า +เขา +อีก +อาจ +อะไร +ออก +อย่าง +อยู่ +อยาก +หาก +หลาย +หลังจาก +หลัง +หรือ +หนึ่ง +ส่วน +ส่ง +สุด +สําหรับ +ว่า +วัน +ลง +ร่วม +ราย +รับ +ระหว่าง +รวม +ยัง +มี +มาก +มา +พร้อม +พบ +ผ่าน +ผล +บาง +น่า +นี้ +นํา +นั้น +นัก +นอกจาก +ทุก +ที่สุด +ที่ +ทําให้ +ทํา +ทาง +ทั้งนี้ +ทั้ง +ถ้า +ถูก +ถึง +ต้อง +ต่างๆ +ต่าง +ต่อ +ตาม +ตั้งแต่ +ตั้ง +ด้าน +ด้วย +ดัง +ซึ่ง +ช่วง +จึง +จาก +จัด +จะ +คือ +ความ +ครั้ง +คง +ขึ้น +ของ +ขอ +ขณะ +ก่อน +ก็ +การ +กับ +กัน +กว่า +กล่าว diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_tr.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_tr.txt new file mode 100644 index 000000000..84d9408d4 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/stopwords_tr.txt @@ -0,0 +1,212 @@ +# Turkish stopwords from LUCENE-559 +# merged with the list from "Information Retrieval on Turkish Texts" +# (http://www.users.muohio.edu/canf/papers/JASIST2008offPrint.pdf) +acaba +altmış +altı +ama +ancak +arada +aslında +ayrıca +bana +bazı +belki +ben +benden +beni +benim +beri +beş +bile +bin +bir +birçok +biri +birkaç +birkez +birşey +birşeyi +biz +bize +bizden +bizi +bizim +böyle +böylece +bu +buna +bunda +bundan +bunlar +bunları +bunların +bunu +bunun +burada +çok +çünkü +da +daha +dahi +de +defa +değil +diğer +diye +doksan +dokuz +dolayı +dolayısıyla +dört +edecek +eden +ederek +edilecek +ediliyor +edilmesi +ediyor +eğer +elli +en +etmesi +etti +ettiği +ettiğini +gibi +göre +halen +hangi +hatta +hem +henüz +hep +hepsi +her +herhangi +herkesin +hiç +hiçbir +için +iki +ile +ilgili +ise +işte +itibaren +itibariyle +kadar +karşın +katrilyon +kendi +kendilerine +kendini +kendisi +kendisine +kendisini +kez +ki +kim +kimden +kime +kimi +kimse +kırk +milyar +milyon +mu +mü +mı +nasıl +ne +neden +nedenle +nerde +nerede +nereye +niye +niçin +o +olan +olarak +oldu +olduğu +olduğunu +olduklarını +olmadı +olmadığı +olmak +olması +olmayan +olmaz +olsa +olsun +olup +olur +olursa +oluyor +on +ona +ondan +onlar +onlardan +onları +onların +onu +onun +otuz +oysa +öyle +pek +rağmen +sadece +sanki +sekiz +seksen +sen +senden +seni +senin +siz +sizden +sizi +sizin +şey +şeyden +şeyi +şeyler +şöyle +şu +şuna +şunda +şundan +şunları +şunu +tarafından +trilyon +tüm +üç +üzere +var +vardı +ve +veya +ya +yani +yapacak +yapılan +yapılması +yapıyor +yapmak +yaptı +yaptığı +yaptığını +yaptıkları +yedi +yerine +yetmiş +yine +yirmi +yoksa +yüz +zaten diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/userdict_ja.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/userdict_ja.txt new file mode 100644 index 000000000..6f0368e4d --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/lang/userdict_ja.txt @@ -0,0 +1,29 @@ +# +# This is a sample user dictionary for Kuromoji (JapaneseTokenizer) +# +# Add entries to this file in order to override the statistical model in terms +# of segmentation, readings and part-of-speech tags. Notice that entries do +# not have weights since they are always used when found. This is by-design +# in order to maximize ease-of-use. +# +# Entries are defined using the following CSV format: +# , ... , ... , +# +# Notice that a single half-width space separates tokens and readings, and +# that the number tokens and readings must match exactly. +# +# Also notice that multiple entries with the same is undefined. +# +# Whitespace only lines are ignored. Comments are not allowed on entry lines. +# + +# Custom segmentation for kanji compounds +日本経済新聞,日本 経済 新聞,ニホン ケイザイ シンブン,カスタム名詞 +関西国際空港,関西 国際 空港,カンサイ コクサイ クウコウ,カスタム名詞 + +# Custom segmentation for compound katakana +トートバッグ,トート バッグ,トート バッグ,かずカナ名詞 +ショルダーバッグ,ショルダー バッグ,ショルダー バッグ,かずカナ名詞 + +# Custom reading for former sumo wrestler +朝青龍,朝青龍,アサショウリュウ,カスタム人名 diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema new file mode 100644 index 000000000..39c811f83 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/managed-schema @@ -0,0 +1,424 @@ + + + + __indexrecordidentifier + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/params.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/params.json new file mode 100644 index 000000000..06114ef25 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/params.json @@ -0,0 +1,20 @@ +{"params":{ + "query":{ + "defType":"edismax", + "q.alt":"*:*", + "rows":"10", + "fl":"*,score", + "":{"v":0} + }, + "facets":{ + "facet":"on", + "facet.mincount": "1", + "":{"v":0} + }, + "velocity":{ + "wt": "velocity", + "v.template":"browse", + "v.layout": "layout", + "":{"v":0} + } +}} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/protwords.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/protwords.txt new file mode 100644 index 000000000..1dfc0abec --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/protwords.txt @@ -0,0 +1,21 @@ +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +#----------------------------------------------------------------------- +# Use a protected word file to protect against the stemmer reducing two +# unrelated words to the same base word. + +# Some non-words that normally won't be encountered, +# just to test that they won't be stemmed. +dontstems +zwhacky + diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/solrconfig.xml b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/solrconfig.xml new file mode 100644 index 000000000..de38e7307 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/solrconfig.xml @@ -0,0 +1,1506 @@ + + + + + + + + + 7.5.0 + + + + + + + + + + + + + + + + + + + + + ${solr.data.dir:} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${solr.lock.type:native} + + + + + + + + + + + + + + + + + + + + + + + + + + + + + ${solr.ulog.dir:} + ${solr.ulog.numVersionBuckets:65536} + + + + + ${solr.autoCommit.maxTime:15000} + false + + + + + + ${solr.autoSoftCommit.maxTime:-1} + + + + + + + + + + + + + + + + 1024 + + + + + + + + + + + + + + + + + + + + + + + + + true + + + + + + 20 + + + 200 + + + + + + + + + + + + + + + + false + + + + + + + + + + + + + + + + + + + + + + + explicit + AND + 10 + + + + + + + + + + + + + + + + explicit + AND + 10 + + + edismax + + + 1.0 + + + + resultidentifier^100 + resultauthor^34 + resultacceptanceyear^21 + resultsubject^13 + resulttitle^8 + relprojectname^5 + resultdescription^3 + __all + + + + + + + + + + + + + + + + + + + + + + + + + + + explicit + json + true + + + + + + + + explicit + + + + + + __all + + + + + + + + + true + ignored_ + __all + + + + + + + + text_general + + + + + + default + __all + solr.DirectSolrSpellChecker + + internal + + 0.5 + + 2 + + 1 + + 5 + + 4 + + 0.01 + + + + + + + + + + + + default + on + true + 10 + 5 + 5 + true + true + 10 + 5 + + + spellcheck + + + + + + + + + + true + + + tvComponent + + + + + + + + + + + + true + false + + + terms + + + + + + + + string + elevate.xml + + + + + + explicit + + + elevator + + + + + + + + + + + 100 + + + + + + + + 70 + + 0.5 + + [-\w ,/\n\"']{20,200} + + + + + + + ]]> + ]]> + + + + + + + + + + + + + + + + + + + + + + + + ,, + ,, + ,, + ,, + ,]]> + ]]> + + + + + + 10 + .,!? + + + + + + + WORD + + + en + US + + + + + + + + + + + + + + [^\w-\.] + _ + + + + + + + yyyy-MM-dd'T'HH:mm:ss.SSSZ + yyyy-MM-dd'T'HH:mm:ss,SSSZ + yyyy-MM-dd'T'HH:mm:ss.SSS + yyyy-MM-dd'T'HH:mm:ss,SSS + yyyy-MM-dd'T'HH:mm:ssZ + yyyy-MM-dd'T'HH:mm:ss + yyyy-MM-dd'T'HH:mmZ + yyyy-MM-dd'T'HH:mm + yyyy-MM-dd HH:mm:ss.SSSZ + yyyy-MM-dd HH:mm:ss,SSSZ + yyyy-MM-dd HH:mm:ss.SSS + yyyy-MM-dd HH:mm:ss,SSS + yyyy-MM-dd HH:mm:ssZ + yyyy-MM-dd HH:mm:ss + yyyy-MM-dd HH:mmZ + yyyy-MM-dd HH:mm + yyyy-MM-dd + + + + strings + + java.lang.Boolean + booleans + + + java.util.Date + tdates + + + java.lang.Long + java.lang.Integer + tlongs + + + java.lang.Number + tdoubles + + + + + + + + + + + + + + + + + + + + + + + + text/plain; charset=UTF-8 + + + + + ${velocity.template.base.dir:} + ${velocity.solr.resource.loader.enabled:true} + ${velocity.params.resource.loader.enabled:false} + + + + + 5 + + + + + + + + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/stopwords.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/stopwords.txt new file mode 100644 index 000000000..ae1e83eeb --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/stopwords.txt @@ -0,0 +1,14 @@ +# Licensed to the Apache Software Foundation (ASF) under one or more +# contributor license agreements. See the NOTICE file distributed with +# this work for additional information regarding copyright ownership. +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/synonyms.txt b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/synonyms.txt new file mode 100644 index 000000000..eab4ee875 --- /dev/null +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/solr/conf/exploreTestConfig/synonyms.txt @@ -0,0 +1,29 @@ +# The ASF licenses this file to You under the Apache License, Version 2.0 +# (the "License"); you may not use this file except in compliance with +# the License. You may obtain a copy of the License at +# +# http://www.apache.org/licenses/LICENSE-2.0 +# +# Unless required by applicable law or agreed to in writing, software +# distributed under the License is distributed on an "AS IS" BASIS, +# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. +# See the License for the specific language governing permissions and +# limitations under the License. + +#----------------------------------------------------------------------- +#some test synonym mappings unlikely to appear in real input text +aaafoo => aaabar +bbbfoo => bbbfoo bbbbar +cccfoo => cccbar cccbaz +fooaaa,baraaa,bazaaa + +# Some synonym groups specific to this example +GB,gib,gigabyte,gigabytes +MB,mib,megabyte,megabytes +Television, Televisions, TV, TVs +#notice we use "gib" instead of "GiB" so any WordDelimiterGraphFilter coming +#after us won't split it into two words. + +# Synonym mappings can be used for spelling correction too +pixima => pixma + diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh index 2a40eb920..b66ab47e0 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/contexts.sh @@ -11,9 +11,13 @@ TARGET_DB=$2 TMP=/tmp/stats-update-`tr -dc A-Za-z0-9 contexts.csv + +echo "Downloading categories data" cat contexts.csv | cut -d , -f1 | xargs -I {} curl -L ${CONTEXT_API}/context/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split(":")[0]),\(.id),\(.label)"' > categories.csv + +echo "Downloading concepts data" cat categories.csv | cut -d , -f2 | sed 's/:/%3A/g'| xargs -I {} curl -L ${CONTEXT_API}/context/category/{}/?all=true | /usr/local/sbin/jq -r '.[]|"\(.id|split("::")[0])::\(.id|split("::")[1]),\(.id),\(.label)"' > concepts.csv cat contexts.csv | sed 's/^\(.*\),\(.*\)/\1,\1::other,\2/' >> categories.csv cat categories.csv | sed 's/^.*,\(.*\),\(.*\)/\1,\1::other,\2/' >> concepts.csv diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index d39af37d5..f4fb2a174 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -11,7 +11,7 @@ create view if not exists TARGET.funder as select * from SOURCE.funder; create view if not exists TARGET.fundref as select * from SOURCE.fundref; create view if not exists TARGET.rndexpenditure as select * from SOURCE.rndexpediture; -create table TARGET.result as +create table TARGET.result stored as parquet as select distinct * from ( select * from SOURCE.result r where exists (select 1 from SOURCE.result_projects rp join SOURCE.project p on rp.project=p.id where rp.id=r.id) union all @@ -21,61 +21,62 @@ create table TARGET.result as 'openorgs____::759d59f05d77188faee99b7493b46805', 'openorgs____::b84450f9864182c67b8611b5593f4250', 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', - 'openorgs____::eadc8da90a546e98c03f896661a2e4d4') )) foo; + 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', + 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2') )) foo; compute stats TARGET.result; -create table TARGET.result_citations as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_citations; -create table TARGET.result_classifications as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_classifications; -create table TARGET.result_concepts as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_concepts; -create table TARGET.result_datasources as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_datasources stored as parquet as select * from SOURCE.result_datasources orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_datasources; -create table TARGET.result_fundercount as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_fundercount stored as parquet as select * from SOURCE.result_fundercount orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_fundercount; -create table TARGET.result_gold as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_gold stored as parquet as select * from SOURCE.result_gold orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_gold; -create table TARGET.result_greenoa as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_greenoa stored as parquet as select * from SOURCE.result_greenoa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_greenoa; -create table TARGET.result_languages as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_languages stored as parquet as select * from SOURCE.result_languages orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_languages; -create table TARGET.result_licences as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_licences stored as parquet as select * from SOURCE.result_licenses orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_licences; -create table TARGET.result_oids as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_oids stored as parquet as select * from SOURCE.result_oids orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_oids; -create table TARGET.result_organization as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_organization stored as parquet as select * from SOURCE.result_organization orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_organization; -create table TARGET.result_peerreviewed as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_peerreviewed stored as parquet as select * from SOURCE.result_peerreviewed orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_peerreviewed; -create table TARGET.result_pids as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_pids stored as parquet as select * from SOURCE.result_pids orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_pids; -create table TARGET.result_projectcount as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_projectcount stored as parquet as select * from SOURCE.result_projectcount orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_projectcount; -create table TARGET.result_projects as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_projects stored as parquet as select * from SOURCE.result_projects orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_projects; -create table TARGET.result_refereed as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_refereed stored as parquet as select * from SOURCE.result_refereed orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_refereed; -create table TARGET.result_sources as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_sources stored as parquet as select * from SOURCE.result_sources orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_sources; -create table TARGET.result_topics as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; -- datasources @@ -84,7 +85,7 @@ create view if not exists TARGET.datasource_oids as select * from SOURCE.datasou create view if not exists TARGET.datasource_organizations as select * from SOURCE.datasource_organizations; create view if not exists TARGET.datasource_sources as select * from SOURCE.datasource_sources; -create table TARGET.datasource_results as select id as result, datasource as id from TARGET.result_datasources; +create table TARGET.datasource_results stored as parquet as select id as result, datasource as id from TARGET.result_datasources; compute stats TARGET.datasource_results; -- organizations @@ -100,7 +101,7 @@ create view if not exists TARGET.project_oids as select * from SOURCE.project_oi create view if not exists TARGET.project_organizations as select * from SOURCE.project_organizations; create view if not exists TARGET.project_resultcount as select * from SOURCE.project_resultcount; -create table TARGET.project_results as select id as result, project as id from TARGET.result_projects; +create table TARGET.project_results stored as parquet as select id as result, project as id from TARGET.result_projects; compute stats TARGET.project_results; -- indicators @@ -121,19 +122,19 @@ create view TARGET.indi_pub_avg_year_content_oa as select * from SOURCE.indi_pub create view TARGET.indi_pub_avg_year_context_oa as select * from SOURCE.indi_pub_avg_year_context_oa orig; create view TARGET.indi_pub_avg_year_country_oa as select * from SOURCE.indi_pub_avg_year_country_oa orig; -create table TARGET.indi_pub_green_oa as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_green_oa stored as parquet as select * from SOURCE.indi_pub_green_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_green_oa; -create table TARGET.indi_pub_grey_lit as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_grey_lit stored as parquet as select * from SOURCE.indi_pub_grey_lit orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_grey_lit; -create table TARGET.indi_pub_doi_from_crossref as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_doi_from_crossref stored as parquet as select * from SOURCE.indi_pub_doi_from_crossref orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_doi_from_crossref; -create table TARGET.indi_pub_gold_oa as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_gold_oa stored as parquet as select * from SOURCE.indi_pub_gold_oa orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_gold_oa; -create table TARGET.indi_pub_has_abstract as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_has_abstract stored as parquet as select * from SOURCE.indi_pub_has_abstract orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_abstract; -create table TARGET.indi_pub_has_cc_licence as select * from SOURCE.indi_pub_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_has_cc_licence stored as parquet as select * from SOURCE.indi_pub_has_cc_licence orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_cc_licence; -create table TARGET.indi_pub_has_cc_licence_url as select * from SOURCE.indi_pub_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); +create table TARGET.indi_pub_has_cc_licence_url stored as parquet as select * from SOURCE.indi_pub_has_cc_licence_url orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.indi_pub_has_cc_licence_url; create view TARGET.indi_software_avg_year_content_oa as select * from SOURCE.indi_software_avg_year_content_oa orig; @@ -143,15 +144,15 @@ create view TARGET.indi_software_avg_year_country_oa as select * from SOURCE.ind --denorm alter table TARGET.result rename to TARGET.res_tmp; -create table TARGET.result_denorm as +create table TARGET.result_denorm stored as parquet as select distinct r.*, rp.project, p.acronym as pacronym, p.title as ptitle, p.funder as pfunder, p.funding_lvl0 as pfunding_lvl0, rd.datasource, d.name as dname, d.type as dtype from TARGET.res_tmp r - join TARGET.result_projects rp on rp.id=r.id - join TARGET.result_datasources rd on rd.id=r.id - join TARGET.project p on p.id=rp.project - join TARGET.datasource d on d.id=rd.datasource; + left outer join TARGET.result_projects rp on rp.id=r.id + left outer join TARGET.result_datasources rd on rd.id=r.id + left outer join TARGET.project p on p.id=rp.project + left outer join TARGET.datasource d on d.id=rd.datasource; compute stats TARGET.result_denorm; alter table TARGET.result_denorm rename to TARGET.result; drop table TARGET.res_tmp; ---- done! +--- done! \ No newline at end of file diff --git a/dhp-workflows/pom.xml b/dhp-workflows/pom.xml index 22ee77619..53d029467 100644 --- a/dhp-workflows/pom.xml +++ b/dhp-workflows/pom.xml @@ -15,6 +15,13 @@ This module is the container for the oozie workflow definitions in dnet-hadoop project + + + DHPSite + ${dhp.site.stage.path}/dhp-workflows + + + dhp-workflow-profiles dhp-aggregation diff --git a/dhp-workflows/src/site/site.xml b/dhp-workflows/src/site/site.xml new file mode 100644 index 000000000..6b742db6a --- /dev/null +++ b/dhp-workflows/src/site/site.xml @@ -0,0 +1,25 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + + + + + \ No newline at end of file diff --git a/pom.xml b/pom.xml index 61b0ad873..9e9bbaa16 100644 --- a/pom.xml +++ b/pom.xml @@ -550,7 +550,7 @@ org.apache.maven.plugins maven-site-plugin - 3.7.1 + 3.9.1 @@ -719,6 +719,10 @@ dnet45-releases https://maven.d4science.org/nexus/content/repositories/dnet45-releases + + DHPSite + ${dhp.site.stage.path}/ + @@ -734,6 +738,7 @@ + sftp://dnet-hadoop@static-web.d4science.org/dnet-hadoop UTF-8 UTF-8 3.6.0 @@ -753,7 +758,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.7.18] + [2.8.22] [4.0.3] [6.0.5] [3.1.6] diff --git a/src/site/site.xml b/src/site/site.xml new file mode 100644 index 000000000..634a2c154 --- /dev/null +++ b/src/site/site.xml @@ -0,0 +1,21 @@ + + + + org.apache.maven.skins + maven-fluido-skin + 1.8 + + + + + + + + + + + + \ No newline at end of file