diff --git a/dhp-common/src/test/resources/eu/dnetlib/dhp/transform/terms.txt b/dhp-common/src/test/resources/eu/dnetlib/dhp/transform/terms.txt index 93cc00eca4..30138b5bcf 100644 --- a/dhp-common/src/test/resources/eu/dnetlib/dhp/transform/terms.txt +++ b/dhp-common/src/test/resources/eu/dnetlib/dhp/transform/terms.txt @@ -1009,7 +1009,7 @@ datacite:id_typologies @=@ datacite:id_typologies @=@ EAN13 @=@ EAN13 datacite:id_typologies @=@ datacite:id_typologies @=@ EISSN @=@ EISSN datacite:id_typologies @=@ datacite:id_typologies @=@ Handle @=@ Handle datacite:id_typologies @=@ datacite:id_typologies @=@ ISBN @=@ ISBN -datacite:id_typologies @=@ datacite:id_typologies @=@ ISSN @=@ ISSN +datacite:id_typologies @=@ datacite:id_typologies @=@ issn @=@ issn datacite:id_typologies @=@ datacite:id_typologies @=@ ISTC @=@ ISTC datacite:id_typologies @=@ datacite:id_typologies @=@ LISSN @=@ LISSN datacite:id_typologies @=@ datacite:id_typologies @=@ LSID @=@ LSID diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_itgv4.xml b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_itgv4.xml index 06325810b4..b421f1342a 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_itgv4.xml +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/input_itgv4.xml @@ -31,7 +31,7 @@ https://pub.uni-bielefeld.de/record/1997560.json - 0016-9056 + 0016-9056 ger Friedrich diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/scripts/original/dc_cleaning_OPENAIREplus_compliant_hal_orig b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/scripts/original/dc_cleaning_OPENAIREplus_compliant_hal_orig index d4eb71dc42..505f562941 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/scripts/original/dc_cleaning_OPENAIREplus_compliant_hal_orig +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/scripts/original/dc_cleaning_OPENAIREplus_compliant_hal_orig @@ -134,9 +134,9 @@ oaf:identifier = set(xpath:"//dri:recordIdentifier", @identifierType = "oai-orig oaf:datasourceprefix = xpath:"//oaf:datasourceprefix"; // journal data -// avoiding regular expressions, while a) correcting ISSNs with no - or other letters instead of - and b) ignoring any stuff after the ISSN (as e.g. print/online/...) -$varISSN = xpath:"//dc:source[starts-with(., 'ISSN:') and string-length(.) > 12]/concat(substring(normalize-space(substring-after(., 'ISSN:')), 1, 4), '-', normalize-space(substring-after(., substring(normalize-space(substring-after(., 'ISSN:')), 1, 4))))"; -//$varEISSN = xpath:"//dc:source[starts-with(., 'EISSN:') and string-length(.) > 13]/normalize-space(substring-after(., 'ISSN:'))"; +// avoiding regular expressions, while a) correcting ISSNs with no - or other letters instead of - and b) ignoring any stuff after the issn (as e.g. print/online/...) +$varISSN = xpath:"//dc:source[starts-with(., 'issn:') and string-length(.) > 12]/concat(substring(normalize-space(substring-after(., 'issn:')), 1, 4), '-', normalize-space(substring-after(., substring(normalize-space(substring-after(., 'issn:')), 1, 4))))"; +//$varEISSN = xpath:"//dc:source[starts-with(., 'EISSN:') and string-length(.) > 13]/normalize-space(substring-after(., 'issn:'))"; $varEISSN = xpath:"//dc:source[starts-with(., 'EISSN:') and string-length(.) > 13]/concat(substring(normalize-space(substring-after(., 'EISSN:')), 1, 4), '-', normalize-space(substring-after(., substring(normalize-space(substring-after(., 'EISSN:')), 1, 4))))"; oaf:journal = set(xpath:"//oaf:datasourceprefix[$varISSN or $varEISSN]/''", @issn = xpath:"$varISSN";, @eissn = xpath:"$varEISSN";); diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/scripts/original/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid_orig.xsl b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/scripts/original/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid_orig.xsl index 3cfaec80b1..f80c91a6a2 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/scripts/original/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid_orig.xsl +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/scripts/original/xslt_cleaning_oaiOpenaire_datacite_ExchangeLandingpagePid_orig.xsl @@ -169,7 +169,7 @@ @@ -283,7 +283,7 @@ - + - + - + @@ -793,9 +793,9 @@ - + - + @@ -844,7 +844,7 @@ - + - + - + @@ -594,9 +594,9 @@ - + - + diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt index 93cc00eca4..30138b5bcf 100644 --- a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt +++ b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/transform/terms.txt @@ -1009,7 +1009,7 @@ datacite:id_typologies @=@ datacite:id_typologies @=@ EAN13 @=@ EAN13 datacite:id_typologies @=@ datacite:id_typologies @=@ EISSN @=@ EISSN datacite:id_typologies @=@ datacite:id_typologies @=@ Handle @=@ Handle datacite:id_typologies @=@ datacite:id_typologies @=@ ISBN @=@ ISBN -datacite:id_typologies @=@ datacite:id_typologies @=@ ISSN @=@ ISSN +datacite:id_typologies @=@ datacite:id_typologies @=@ issn @=@ issn datacite:id_typologies @=@ datacite:id_typologies @=@ ISTC @=@ ISTC datacite:id_typologies @=@ datacite:id_typologies @=@ LISSN @=@ LISSN datacite:id_typologies @=@ datacite:id_typologies @=@ LSID @=@ LSID diff --git a/dhp-workflows/dhp-doiboost/src/main/resources/eu.dnetlib.dhp.doiboost.mappings/crossref_mapping.csv b/dhp-workflows/dhp-doiboost/src/main/resources/eu.dnetlib.dhp.doiboost.mappings/crossref_mapping.csv index 6a5fc3f871..0c1fd9e64b 100644 --- a/dhp-workflows/dhp-doiboost/src/main/resources/eu.dnetlib.dhp.doiboost.mappings/crossref_mapping.csv +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu.dnetlib.dhp.doiboost.mappings/crossref_mapping.csv @@ -36,10 +36,10 @@ article-number,String,No,,N/A, published-print,Partial Date,No,Date on which the work was published in print,"Result/relevantDate with Qualifier(""published-print"", ""dnet:dataCite_date"")", published-online,Partial Date,No,Date on which the work was published online,"Result/relevantDate with Qualifier(""published-online"", ""dnet:dataCite_date"")", subject,Array of String,No,"Subject category names, a controlled vocabulary from Sci-Val. Available for most journal articles","Result/subject with Qualifier(""keywords"", ""dnet:subject_classification_typologies""). ","Future improvements: map the controlled vocabulary instead of using the generic ""keywords"" qualifier" -ISSN,Array of String,No,,"Publication/Journal/issn +issn,Array of String,No,,"Publication/Journal/issn Publication/Journal/lissn Publication/Journal/eissn",The mapping depends on the value of issn-type -issn-type,Array of ISSN with Type,No,List of ISSNs with ISSN type information,N/A,Its value guides the setting of the properties in Journal (see row above) +issn-type,Array of issn with Type,No,List of ISSNs with issn type information,N/A,Its value guides the setting of the properties in Journal (see row above) ISBN,Array of String,No,,Publication/source,"In case of Book We can map ISBN and container title on Publication/source using this syntax container-title + ""ISBN: "" + ISBN" archive,Array of String,No,,N/A, license,Array of License,No,,Result/Instance/License, diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv index 6d4b6cdcbd..ebde1bf189 100644 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv @@ -1,4 +1,4 @@ -"ISSN","ISSN_L","ISSN_IN_DOAJ","ISSN_IN_ROAD","ISSN_IN_PMC","ISSN_IN_OAPC","ISSN_IN_WOS","ISSN_IN_SCOPUS","JOURNAL_IN_DOAJ","JOURNAL_IN_ROAD","JOURNAL_IN_PMC","JOURNAL_IN_OAPC","JOURNAL_IN_WOS","JOURNAL_IN_SCOPUS","TITLE","TITLE_SOURCE" +"issn","ISSN_L","ISSN_IN_DOAJ","ISSN_IN_ROAD","ISSN_IN_PMC","ISSN_IN_OAPC","ISSN_IN_WOS","ISSN_IN_SCOPUS","JOURNAL_IN_DOAJ","JOURNAL_IN_ROAD","JOURNAL_IN_PMC","JOURNAL_IN_OAPC","JOURNAL_IN_WOS","JOURNAL_IN_SCOPUS","TITLE","TITLE_SOURCE" "0001-625X","0001-625X",1,1,0,0,0,1,1,1,0,0,0,1,"Acta Mycologica","DOAJ" "0002-0397","0002-0397",1,1,0,0,1,1,1,1,0,0,1,1,"Africa Spectrum","DOAJ" "0003-2565","0003-2565",1,0,0,0,0,0,1,0,0,0,0,0,"Anali Pravnog Fakulteta u Beogradu","DOAJ" diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 19febb9ed7..665c01276a 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -122,6 +122,11 @@ org.json4s json4s-jackson_2.11 + + com.opencsv + opencsv + 5.5 + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Aggregators.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Aggregators.scala new file mode 100644 index 0000000000..d984183399 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Aggregators.scala @@ -0,0 +1,54 @@ +package eu.dnetlib.dhp.oa.graph.hostebymap + +import org.apache.spark.sql.{Dataset, Encoder, Encoders, TypedColumn} +import org.apache.spark.sql.expressions.Aggregator + + +case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {} + + +object Aggregators { + + + + def getId(s1:String, s2:String) : String = { + if (!s1.equals("")){ + return s1} + s2 + } + + + def createHostedByItemTypes(df: Dataset[HostedByItemType]): Dataset[HostedByItemType] = { + val transformedData : Dataset[HostedByItemType] = df + .groupByKey(_.id)(Encoders.STRING) + .agg(Aggregators.hostedByAggregator) + .map{ + case (id:String , res:HostedByItemType) => res + }(Encoders.product[HostedByItemType]) + + transformedData + } + + val hostedByAggregator: TypedColumn[HostedByItemType, HostedByItemType] = new Aggregator[HostedByItemType, HostedByItemType, HostedByItemType] { + override def zero: HostedByItemType = HostedByItemType("","","","","",false) + override def reduce(b: HostedByItemType, a:HostedByItemType): HostedByItemType = { + return merge(b, a) + } + override def merge(b1: HostedByItemType, b2: HostedByItemType): HostedByItemType = { + if (b1 == null){ + return b2 + } + if(b2 == null){ + return b1 + } + + HostedByItemType(getId(b1.id, b2.id), getId(b1.officialname, b2.officialname), getId(b1.issn, b2.issn), getId(b1.eissn, b2.eissn), getId(b1.lissn, b2.lissn), b1.openAccess || b2.openAccess) + + } + override def finish(reduction: HostedByItemType): HostedByItemType = reduction + override def bufferEncoder: Encoder[HostedByItemType] = Encoders.product[HostedByItemType] + + override def outputEncoder: Encoder[HostedByItemType] = Encoders.product[HostedByItemType] + }.toColumn + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Constants.java new file mode 100644 index 0000000000..b07e33cd19 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Constants.java @@ -0,0 +1,15 @@ +package eu.dnetlib.dhp.oa.graph.hostebymap; + +public class Constants { + + + + public static final String OPENAIRE = "openaire"; + public static final String DOAJ = "doaj"; + public static final String UNIBI = "unibi"; + + + public static final String ISSN = "issn"; + public static final String EISSN = "eissn"; + public static final String ISSNL = "issnl"; +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/GetCSV.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/GetCSV.java new file mode 100644 index 0000000000..d397886a32 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/GetCSV.java @@ -0,0 +1,111 @@ +package eu.dnetlib.dhp.oa.graph.hostebymap; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.opencsv.bean.CsvToBeanBuilder; +import eu.dnetlib.dhp.oa.graph.hostebymap.model.UnibiGoldModel; +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 eu.dnetlib.dhp.application.ArgumentApplicationParser; +import org.apache.hadoop.fs.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.nio.charset.Charset; +import java.nio.charset.StandardCharsets; +import java.util.List; +import java.util.Optional; + +public class GetCSV { + private static final Log log = LogFactory.getLog(eu.dnetlib.dhp.oa.graph.hostebymap.GetCSV.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GetCSV.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/hostedbymap/download_csv_parameters.json"))); + + parser.parseArgument(args); + + final String fileURL = parser.get("fileURL"); + final String hdfsPath = parser.get("hdfsPath"); + final String hdfsNameNode = parser.get("hdfsNameNode"); + final String classForName = parser.get("classForName"); + final Boolean shouldReplace = Optional.ofNullable((parser.get("replace"))) + .map(Boolean::valueOf) + .orElse(false); + + + URLConnection connection = new URL(fileURL).openConnection(); + connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11"); + connection.connect(); + + BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream(), Charset.forName("UTF-8"))); + + if(shouldReplace){ + PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter("/tmp/DOAJ.csv"))); + String line = null; + while((line = in.readLine())!= null){ + writer.println(line.replace("\\\"", "\"")); + } + writer.close(); + in.close(); + in = new BufferedReader(new FileReader("/tmp/DOAJ.csv")); + } + + Configuration conf = new Configuration(); + conf.set("fs.defaultFS", hdfsNameNode); + + FileSystem fileSystem = FileSystem.get(conf); + Path hdfsWritePath = new Path(hdfsPath); + FSDataOutputStream fsDataOutputStream = null; + if (fileSystem.exists(hdfsWritePath)) { + fileSystem.delete(hdfsWritePath, false); + } + fsDataOutputStream = fileSystem.create(hdfsWritePath); + + BufferedWriter writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); + + Class clazz = Class.forName(classForName); + + ObjectMapper mapper = new ObjectMapper(); + + new CsvToBeanBuilder(in) + .withType(clazz) + .withMultilineLimit(1) + .build() + .parse() + .forEach(line -> { + try { + writer.write(mapper.writeValueAsString(line)); + writer.newLine(); + } catch (IOException e) { + throw new RuntimeException(e); + } + }); + + + + writer.close(); + in.close(); + if(shouldReplace){ + File f = new File("/tmp/DOAJ.csv"); + f.delete(); + } + + + } + + + + +} + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/SparkPrepareHostedByMapData.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/SparkPrepareHostedByMapData.scala new file mode 100644 index 0000000000..55b6e36cd0 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/SparkPrepareHostedByMapData.scala @@ -0,0 +1,158 @@ +package eu.dnetlib.dhp.oa.graph.hostebymap + +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.graph.hostebymap.model.{DOAJModel, UnibiGoldModel} +import eu.dnetlib.dhp.oa.merge.AuthorMerger +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{Datasource, Organization, Publication, Relation} +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.json4s.DefaultFormats +import org.slf4j.{Logger, LoggerFactory} +import org.json4s.jackson.Serialization.write + +import scala.collection.mutable.ListBuffer + +object SparkPrepareHostedByMapData { + + case class HostedByInfo(id: Option[String], officialname: String, journal_id: String, provenance : String, id_type: String) {} + + implicit val tupleForJoinEncoder: Encoder[(String, HostedByItemType)] = Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType]) + implicit val mapEncoderDats: Encoder[Datasource] = Encoders.bean(classOf[Datasource]) + implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel] + implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel] + implicit val mapEncoderHBI: Encoder[HostedByInfo] = Encoders.product[HostedByInfo] + + + def toHostedByItemType(input: ((HostedByInfo, HostedByInfo), HostedByInfo)) : HostedByItemType = { + val openaire: HostedByInfo = input._1._1 + val doaj: HostedByInfo = input._1._2 + val gold: HostedByInfo = input._2 + val isOpenAccess: Boolean = doaj == null && gold == null + + openaire.journal_id match { + case Constants.ISSN => return HostedByItemType(openaire.id.get, openaire.officialname, openaire.journal_id, "", "", isOpenAccess) + case Constants.EISSN => return HostedByItemType(openaire.id.get, openaire.officialname, "", openaire.journal_id, "", isOpenAccess) + case Constants.ISSNL => return HostedByItemType(openaire.id.get, openaire.officialname, "", "", openaire.journal_id, isOpenAccess) + + // catch the default with a variable so you can print it + case whoa => return null + } + } + + def toHostedByMap(input: HostedByItemType): ListBuffer[String] = { + implicit val formats = DefaultFormats + val serializedJSON:String = write(input) + + var hostedBy = new ListBuffer[String]() + if(!input.issn.equals("")){ + hostedBy += "{\"" + input.issn + "\":" + serializedJSON + "}" + } + if(!input.eissn.equals("")){ + hostedBy += "{\"" + input.eissn + "\":" + serializedJSON + "}" + } + if(!input.lissn.equals("")){ + hostedBy += "{\"" + input.lissn + "\":" + serializedJSON + "}" + } + + hostedBy + + } + + + def readOADataset(input:String, spark: SparkSession): Dataset[HostedByInfo] = { + spark.read.textFile(input).as[Datasource].flatMap(ds => { + val lst = new ListBuffer[HostedByInfo]() + if (ds.getJournal == null) { + return null + } + val issn: String = ds.getJournal.getIssnPrinted + val issnl: String = ds.getJournal.getIssnOnline + val eissn: String = ds.getJournal.getIssnOnline + val id: String = ds.getId + val officialname: String = ds.getOfficialname.getValue + if (issn != null) { + lst += HostedByInfo(Some(id), officialname, issn, Constants.OPENAIRE, Constants.ISSN) + } + if (issnl != null) { + lst += HostedByInfo(Some(id), officialname, issnl, Constants.OPENAIRE, Constants.ISSNL) + } + if (eissn != null) { + lst += HostedByInfo(Some(id), officialname, eissn, Constants.OPENAIRE, Constants.EISSN) + } + lst + }).filter(i => i != null) + } + + def main(args: Array[String]): Unit = { + + val logger: Logger = LoggerFactory.getLogger(getClass) + val conf: SparkConf = new SparkConf() + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/hostedby/prepare_hostedby_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + import spark.implicits._ + + val datasourcePath = parser.get("datasourcePath") + val workingDirPath = parser.get("workingPath") + + + + + logger.info("Getting the Datasources") + + val doajDataset: Dataset[DOAJModel] = spark.read.load(workingDirPath + "/doaj").as[DOAJModel] + val unibiDataset: Dataset[UnibiGoldModel] = spark.read.load(datasourcePath).as[UnibiGoldModel] + + val oa: Dataset[HostedByInfo] = readOADataset(datasourcePath, spark) + + val doaj: Dataset[HostedByInfo] = doajDataset.flatMap(doaj => { + val lst = new ListBuffer[HostedByInfo]() + val issn: String = doaj.getIssn + val eissn: String = doaj.getEissn + val officialname: String = doaj.getJournalTitle + if (issn != null) { + lst += HostedByInfo(null, officialname, issn, Constants.DOAJ, Constants.ISSN) + } + if (eissn != null) { + lst += HostedByInfo(null, officialname, eissn, Constants.DOAJ, Constants.EISSN) + } + lst + }) + + val gold: Dataset[HostedByInfo] = unibiDataset.flatMap(gold => { + val lst = new ListBuffer[HostedByInfo]() + val issn: String = gold.getIssn + val issnl: String = gold.getIssn_l + val officialname: String = gold.getTitle + if (issn != null) { + lst += HostedByInfo(null, officialname, issn, Constants.UNIBI, Constants.ISSN) + } + if (issnl != null) { + lst += HostedByInfo(null, officialname, issnl, Constants.UNIBI, Constants.ISSNL) + } + lst + }) + + Aggregators.createHostedByItemTypes(oa.joinWith(doaj, oa.col("journal_id").equalTo(doaj.col("journal_id")), "left") + .joinWith(gold, $"_1.col('journal_id')".equalTo(gold.col("journal_id")), "left").map(toHostedByItemType) + .filter(i => i != null)) + .flatMap(toHostedByMap) + // .map(i => (i.id,i)) + // .groupByKey(_._1) + // .agg(hostedByAggregator.toColumn) + // .map(p => p._2) + .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/HostedByMap") + + + } + + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/DOAJModel.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/DOAJModel.java new file mode 100644 index 0000000000..fe1d14a763 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/DOAJModel.java @@ -0,0 +1,53 @@ +package eu.dnetlib.dhp.oa.graph.hostebymap.model; + +import java.io.Serializable; + +import com.opencsv.bean.CsvBindByName; + + +public class DOAJModel implements Serializable { + @CsvBindByName(column = "Journal title") + private String journalTitle; + + @CsvBindByName(column = "Journal ISSN (print version)") + private String issn ; + + @CsvBindByName(column = "Journal EISSN (online version)") + private String eissn; + + @CsvBindByName(column = "Review process") + private String reviewProcess; + + + public String getJournalTitle() { + return journalTitle; + } + + public void setJournalTitle(String journalTitle) { + this.journalTitle = journalTitle; + } + + public String getIssn() { + return issn; + } + + public void setIssn(String issn) { + this.issn = issn; + } + + public String getEissn() { + return eissn; + } + + public void setEissn(String eissn) { + this.eissn = eissn; + } + + public String getReviewProcess() { + return reviewProcess; + } + + public void setReviewProcess(String reviewProcess) { + this.reviewProcess = reviewProcess; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/UnibiGoldModel.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/UnibiGoldModel.java new file mode 100644 index 0000000000..309f74eea5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/UnibiGoldModel.java @@ -0,0 +1,44 @@ +package eu.dnetlib.dhp.oa.graph.hostebymap.model; + +import com.opencsv.bean.CsvBindByName; + +import java.io.Serializable; + +public class UnibiGoldModel implements Serializable { + @CsvBindByName(column = "ISSN") + private String issn; + @CsvBindByName(column = "ISSN_L") + private String issn_l; + @CsvBindByName(column = "TITLE") + private String title; + @CsvBindByName(column = "TITLE_SOURCE") + private String title_source; + + public String getIssn() { + return issn; + } + + public void setIssn(String issn) { + this.issn = issn; + } + + public String getIssn_l() { + return issn_l; + } + + public String getTitle() { + return title; + } + + public void setTitle(String title) { + this.title = title; + } + + public String getTitle_source() { + return title_source; + } + + public void setTitle_source(String title_source) { + this.title_source = title_source; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPreprocess.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPreprocess.scala new file mode 100644 index 0000000000..657f20fce4 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPreprocess.scala @@ -0,0 +1,59 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap + +import java.sql.Timestamp + +import eu.dnetlib.dhp.oa.graph.hostebymap.SparkPrepareHostedByMapData +import eu.dnetlib.dhp.oa.graph.hostebymap.SparkPrepareHostedByMapData.HostedByInfo +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, SparkSession} +import org.codehaus.jackson.map.ObjectMapper +import org.json4s.DefaultFormats +import org.junit.jupiter.api.Assertions.{assertNotNull, assertTrue} +import org.junit.jupiter.api.Test +import org.slf4j.{Logger, LoggerFactory} + +import scala.io.Source + +class TestPreprocess { + + val logger: Logger = LoggerFactory.getLogger(getClass) + val mapper = new ObjectMapper() + + + + @Test + def readDatasource():Unit = { + + + import org.apache.spark.sql.Encoders + implicit val formats = DefaultFormats + import org.json4s.jackson.Serialization.write + + val conf = new SparkConf() + conf.setMaster("local[*]") + conf.set("spark.driver.host", "localhost") + val spark: SparkSession = + SparkSession + .builder() + .appName(getClass.getSimpleName) + .config(conf) + .getOrCreate() + val path = getClass.getResource("datasource.json").getPath + + + val schema = Encoders.product[HostedByInfo] + + spark.read.textFile(path).foreach(r => println(mapper.writeValueAsString(r))) + +// SparkPrepareHostedByMapData.readOADataset(path, spark) +// .foreach(r => println(write(r))) + + + spark.close() + } + + + + + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestReadCSV.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestReadCSV.java new file mode 100644 index 0000000000..01c70502c7 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestReadCSV.java @@ -0,0 +1,111 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; +import com.opencsv.bean.CsvToBeanBuilder; +import eu.dnetlib.dhp.oa.graph.hostebymap.GetCSV; +import eu.dnetlib.dhp.oa.graph.hostebymap.model.UnibiGoldModel; +import org.junit.jupiter.api.Test; + +import java.io.*; +import java.net.MalformedURLException; +import java.net.URL; +import java.net.URLConnection; +import java.nio.charset.Charset; +import java.nio.charset.StandardCharsets; +import java.util.List; + +public class TestReadCSV { + + @Test + public void testCSVUnibi() throws FileNotFoundException { + + + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/hostedbymap/unibiGold.csv") + .getPath(); + + List beans = new CsvToBeanBuilder(new FileReader(sourcePath)) + .withType(UnibiGoldModel.class) + .build() + .parse(); + + ObjectMapper mapper = new ObjectMapper(); + + beans.forEach(r -> { + try { + System.out.println(mapper.writeValueAsString(r)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); + + + } + + @Test + public void testCSVUrlUnibi() throws IOException { + + URL csv = new URL("https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_4.csv"); + + BufferedReader in = new BufferedReader(new InputStreamReader(csv.openStream())); + ObjectMapper mapper = new ObjectMapper(); + + new CsvToBeanBuilder(in) + .withType(eu.dnetlib.dhp.oa.graph.hostebymap.model.UnibiGoldModel.class) + .build() + .parse() + .forEach(line -> + + { + try { + System.out.println(mapper.writeValueAsString(line)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + } + + + ); + } + + @Test + public void testCSVUrlDOAJ() throws IOException { + + URLConnection connection = new URL("https://doaj.org/csv").openConnection(); + connection.setRequestProperty("User-Agent", "Mozilla/5.0 (Windows NT 6.1; WOW64) AppleWebKit/537.11 (KHTML, like Gecko) Chrome/23.0.1271.95 Safari/537.11"); + connection.connect(); + + BufferedReader in = new BufferedReader(new InputStreamReader(connection.getInputStream(), Charset.forName("UTF-8"))); + //BufferedReader in = new BufferedReader(new FileReader("/tmp/DOAJ.csv")); + PrintWriter writer = new PrintWriter(new BufferedWriter(new FileWriter("/tmp/DOAJ_1.csv"))); + String line = null; + while((line = in.readLine())!= null){ + writer.println(line.replace("\\\"", "\"")); + } + writer.close(); + in.close(); + in = new BufferedReader(new FileReader("/tmp/DOAJ_1.csv")); + ObjectMapper mapper = new ObjectMapper(); + + + + new CsvToBeanBuilder(in) + .withType(eu.dnetlib.dhp.oa.graph.hostebymap.model.DOAJModel.class) + .withMultilineLimit(1) + .build() + .parse() + .forEach(lline -> + + { + try { + System.out.println(mapper.writeValueAsString(lline)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + } + + + ); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt index ba47aaf5c8..4db5fd463d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt @@ -1009,7 +1009,7 @@ datacite:id_typologies @=@ datacite:id_typologies @=@ EAN13 @=@ EAN13 datacite:id_typologies @=@ datacite:id_typologies @=@ EISSN @=@ EISSN datacite:id_typologies @=@ datacite:id_typologies @=@ Handle @=@ Handle datacite:id_typologies @=@ datacite:id_typologies @=@ ISBN @=@ ISBN -datacite:id_typologies @=@ datacite:id_typologies @=@ ISSN @=@ ISSN +datacite:id_typologies @=@ datacite:id_typologies @=@ issn @=@ issn datacite:id_typologies @=@ datacite:id_typologies @=@ ISTC @=@ ISTC datacite:id_typologies @=@ datacite:id_typologies @=@ LISSN @=@ LISSN datacite:id_typologies @=@ datacite:id_typologies @=@ LSID @=@ LSID diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json new file mode 100644 index 0000000000..15e1dcc45a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json @@ -0,0 +1,10 @@ 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b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibi_transformed.json new file mode 100644 index 0000000000..d4acba4a9c --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibi_transformed.json @@ -0,0 +1,29 @@ +{"issn":"2502-731X","issn_l":"2502-731X","title":"JIMKESMAS (Jurnal Ilmiah Mahasiswa Kesehatan Masyarakat)","title_source":"ROAD"} +{"issn":"2502-7409","issn_l":"1411-0253","title":"Jurnal ilmu informasi, perpustakaan, dan kearsipan","title_source":"ROAD"} +{"issn":"2502-7433","issn_l":"2502-7433","title":"At-Tadbir : jurnal ilmiah manajemen","title_source":"ROAD"} +{"issn":"2502-745X","issn_l":"2502-745X","title":"Jurnal Kesehatan Panrita Husada.","title_source":"ROAD"} +{"issn":"2502-7549","issn_l":"2502-7549","title":"ELang journal (An English Education journal)","title_source":"ROAD"} +{"issn":"2423-3633","issn_l":"2423-3625","title":"̒Ulūm-i darmāngāhī-i dāmpizishkī-i Īrān.","title_source":"ROAD"} +{"issn":"2423-5563","issn_l":"2423-3773","title":"Pizhūhishnāmah-i ̒ilm/sanjī.","title_source":"ROAD"} +{"issn":"1735-434X","issn_l":"1735-434X","title":"Iranian journal of animal biosystematics.","title_source":"ROAD"} +{"issn":"2423-4435","issn_l":"2008-6113","title":"Majallah-i jangal-i Īrān.","title_source":"ROAD"} +{"issn":"2423-4575","issn_l":"2423-4575","title":"Ābziyān-i zinatī.","title_source":"ROAD"} +{"issn":"2423-4974","issn_l":"2423-4974","title":"Pizhūhishnāmah-i ravābiṭ-i biyn/al- milal.","title_source":"ROAD"} +{"issn":"2380-0607","issn_l":"2380-0607","title":"AIHM journal club.","title_source":"ROAD"} +{"issn":"1085-4568","issn_l":"1085-4568","title":"Frontiers.","title_source":"ROAD"} +{"issn":"2380-8845","issn_l":"2380-8845","title":"˜The œjournal of contemporary archival studies.","title_source":"ROAD"} +{"issn":"2381-1803","issn_l":"2381-1803","title":"International journal of complementary & alternative medicine.","title_source":"ROAD"} +{"issn":"2381-2478","issn_l":"2381-2478","title":"Palapala.","title_source":"ROAD"} +{"issn":"2382-5170","issn_l":"2382-5170","title":"Asia pacific journal of environment ecology and sustainable development.","title_source":"ROAD"} +{"issn":"2382-9737","issn_l":"2382-9737","title":"Majallah-i salāmat va bihdāsht","title_source":"ROAD"} +{"issn":"2382-977X","issn_l":"2382-977X","title":"UCT journal of research in science ,engineering and technology","title_source":"ROAD"} +{"issn":"2382-9974","issn_l":"2382-9974","title":"Bih/nizhādī-i giyāhān-i zirā̒ī va bāghī.","title_source":"ROAD"} +{"issn":"2227-4782","issn_l":"2227-4782","title":"Problemi endokrinnoï patologìï.","title_source":"ROAD"} +{"issn":"2685-0079","issn_l":"2597-4971","title":"Jurnal Kebijakan Pembangunan Daerah : Jurnal Penelitian dan Pengembangan Kebijakan Pembangunan Daerah.","title_source":"ROAD"} +{"issn":"2574-0075","issn_l":"2574-0075","title":"Hypermedia magazine.","title_source":"ROAD"} +{"issn":"2574-0296","issn_l":"2574-0296","title":"˜The œmuseum review.","title_source":"ROAD"} +{"issn":"2574-0334","issn_l":"2574-0334","title":"Bioactive compounds in health and disease.","title_source":"ROAD"} +{"issn":"2574-108X","issn_l":"2574-108X","title":"Journal of computer science integration.","title_source":"ROAD"} +{"issn":"2574-254X","issn_l":"2574-254X","title":"Child and adolescent obesity.","title_source":"ROAD"} +{"issn":"2574-3325","issn_l":"2574-3325","title":"Journal of research on the college president.","title_source":"ROAD"} +{"issn":"2239-6101","issn_l":"2239-5938","title":"European journal of sustainable development.","title_source":"ROAD"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_dedup.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_dedup.xml index 95457fb701..b45fa1edba 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_dedup.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_dedup.xml @@ -16,7 +16,7 @@ Doğuş Üniversitesi, Fen Edebiyat Fakültesi, Fizik Bölümü TR3959 urn:issn:1748-0221 - VOLUME=7;ISSUE=1;ISSN=1748-0221;TITLE=Journal of Instrumentation + VOLUME=7;ISSUE=1;issn=1748-0221;TITLE=Journal of Instrumentation ATLAS Collaboration Mitsou, Vasiliki Fiorini, Luca Ros Martínez, Eduardo Castillo Giménez, María Victoria Fuster Verdú, Juan A. García García, Carmen Cabrera Urbán, Susana Martí García, Salvador Salt Cairols, José Lacasta Llácer, Carlos Valls Ferrer, @@ -30,7 +30,7 @@ interactions. Journal of Instrumentation, 7(1). doi: 10.1088/1748-0221/7/01/P01013. UC Santa Cruz: Retrieved from: http://www.escholarship.org/uc/item/05j2j2br Journal of Instrumentation, 7 - VOLUME=7;ISSN=1748-0221;TITLE=Journal of Instrumentation + VOLUME=7;issn=1748-0221;TITLE=Journal of Instrumentation 1748-0221 Journal of Instrumentation 7, P01013 (2012). doi:10.1088/1748-0221/7/01/P01013 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed.xml index 22da07e299..06ebe97cd5 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/sx/graph/bio/pubmed/pubmed.xml @@ -16,7 +16,7 @@
- 0006-2944 + 0006-2944 13 2 @@ -182,7 +182,7 @@
- 1090-2104 + 1090-2104 66 4 @@ -314,7 +314,7 @@
- 0006-291X + 0006-291X 66 4 @@ -460,7 +460,7 @@
- 1090-2104 + 1090-2104 66 4 @@ -644,7 +644,7 @@
- 1090-2104 + 1090-2104 66 4 @@ -774,7 +774,7 @@
- 0006-291X + 0006-291X 66 4 @@ -934,7 +934,7 @@
- 1873-2968 + 1873-2968 24 16 @@ -1614,7 +1614,7 @@
- 1873-2968 + 1873-2968 24 16 @@ -2017,7 +2017,7 @@
- 0006-2952 + 0006-2952 24 17 @@ -2185,7 +2185,7 @@
- 1873-2968 + 1873-2968 24 17 @@ -2337,7 +2337,7 @@
- 0006-2952 + 0006-2952 24 18 @@ -2585,7 +2585,7 @@
- 0006-2952 + 0006-2952 24 18 @@ -2838,7 +2838,7 @@
- 0006-2952 + 0006-2952 24 18 @@ -3020,7 +3020,7 @@
- 0006-2952 + 0006-2952 24 18 @@ -3204,7 +3204,7 @@
- 0006-2952 + 0006-2952 24 18 @@ -3450,7 +3450,7 @@
- 0006-2952 + 0006-2952 24 18 @@ -3683,7 +3683,7 @@
- 0006-2952 + 0006-2952 24 18 @@ -3880,7 +3880,7 @@
- 0006-2952 + 0006-2952 24 20 @@ -4069,7 +4069,7 @@
- 0006-2952 + 0006-2952 24 20 @@ -4428,7 +4428,7 @@
- 0006-2952 + 0006-2952 24 20 @@ -4590,7 +4590,7 @@
- 0004-4172 + 0004-4172 25 9 @@ -4741,7 +4741,7 @@
- 0004-4172 + 0004-4172 25 9 @@ -4999,7 +4999,7 @@
- 0004-4172 + 0004-4172 25 9 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/transform/terms.txt b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/transform/terms.txt index 93cc00eca4..30138b5bcf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/transform/terms.txt +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/transform/terms.txt @@ -1009,7 +1009,7 @@ datacite:id_typologies @=@ datacite:id_typologies @=@ EAN13 @=@ EAN13 datacite:id_typologies @=@ datacite:id_typologies @=@ EISSN @=@ EISSN datacite:id_typologies @=@ datacite:id_typologies @=@ Handle @=@ Handle datacite:id_typologies @=@ datacite:id_typologies @=@ ISBN @=@ ISBN -datacite:id_typologies @=@ datacite:id_typologies @=@ ISSN @=@ ISSN +datacite:id_typologies @=@ datacite:id_typologies @=@ issn @=@ issn datacite:id_typologies @=@ datacite:id_typologies @=@ ISTC @=@ ISTC datacite:id_typologies @=@ datacite:id_typologies @=@ LISSN @=@ LISSN datacite:id_typologies @=@ datacite:id_typologies @=@ LSID @=@ LSID