From 63553a76b3a9e491672c98177be1883a91035fd8 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 22 Jul 2021 12:01:48 +0200 Subject: [PATCH 01/51] added code to download gold issn list from unibi --- dhp-common/pom.xml | 10 ++ .../project/utils/CSVParser.java | 7 +- .../actionmanager/project/utils/ReadCSV.java | 16 +- .../project/utils/ReadExcel.java | 2 +- .../dhp/actionmanager/project/parameters.json | 5 + dhp-workflows/dhp-doiboost/pom.xml | 7 +- .../main/java/eu/dnetlib/doiboost/GetCSV.java | 37 +++++ .../eu/dnetlib/doiboost/UnibiGoldModel.java | 151 ++++++++++++++++++ .../download_unibi_issn_gold_parameters.json | 39 +++++ .../preprocess/oozie_app/workflow.xml | 14 ++ .../eu/dnetlib/dhp/doiboost/GetCSVTest.java | 43 +++++ .../dhp/doiboost/issn_gold_oa_version_4.csv | 73 +++++++++ .../oa/provision/utils/XmlRecordFactory.java | 2 +- 13 files changed, 398 insertions(+), 8 deletions(-) create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/GetCSV.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/UnibiGoldModel.java create mode 100644 dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_unibi_issn_gold_parameters.json create mode 100644 dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/GetCSVTest.java create mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index 74f31cf357..b32039e327 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -112,6 +112,16 @@ eu.dnetlib.dhp dhp-schemas + + + org.apache.commons + commons-csv + 1.8 + + + + + diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVParser.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVParser.java index 8bdce903b1..1d839bec53 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVParser.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/CSVParser.java @@ -16,10 +16,15 @@ import org.apache.commons.lang.reflect.FieldUtils; public class CSVParser { public List parse(String csvFile, String classForName) + throws ClassNotFoundException, IOException, IllegalAccessException, InstantiationException { + return parse(csvFile, classForName, ';'); + } + + public List parse(String csvFile, String classForName, char delimiter) throws ClassNotFoundException, IOException, IllegalAccessException, InstantiationException { final CSVFormat format = CSVFormat.EXCEL .withHeader() - .withDelimiter(';') + .withDelimiter(delimiter) .withQuote('"') .withTrim(); List ret = new ArrayList<>(); diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java index c73f7ec3d1..f9118350f5 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadCSV.java @@ -6,6 +6,7 @@ import java.io.Closeable; import java.io.IOException; import java.io.OutputStreamWriter; import java.nio.charset.StandardCharsets; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.commons.logging.Log; @@ -29,6 +30,7 @@ public class ReadCSV implements Closeable { private final BufferedWriter writer; private final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); private final String csvFile; + private final char delimiter; public static void main(final String[] args) throws Exception { final ArgumentApplicationParser parser = new ArgumentApplicationParser( @@ -44,19 +46,23 @@ public class ReadCSV implements Closeable { final String hdfsPath = parser.get("hdfsPath"); final String hdfsNameNode = parser.get("hdfsNameNode"); final String classForName = parser.get("classForName"); - - try (final ReadCSV readCSV = new ReadCSV(hdfsPath, hdfsNameNode, fileURL)) { + Optional delimiter = Optional.ofNullable(parser.get("delimiter")); + char del = ';'; + if (delimiter.isPresent()) + del = delimiter.get().charAt(0); + try (final ReadCSV readCSV = new ReadCSV(hdfsPath, hdfsNameNode, fileURL, del)) { log.info("Getting CSV file..."); readCSV.execute(classForName); } + } public void execute(final String classForName) throws Exception { CSVParser csvParser = new CSVParser(); csvParser - .parse(csvFile, classForName) + .parse(csvFile, classForName, delimiter) .stream() .forEach(p -> write(p)); @@ -70,7 +76,8 @@ public class ReadCSV implements Closeable { public ReadCSV( final String hdfsPath, final String hdfsNameNode, - final String fileURL) + final String fileURL, + char delimiter) throws Exception { this.conf = new Configuration(); this.conf.set("fs.defaultFS", hdfsNameNode); @@ -85,6 +92,7 @@ public class ReadCSV implements Closeable { this.writer = new BufferedWriter(new OutputStreamWriter(fsDataOutputStream, StandardCharsets.UTF_8)); this.csvFile = httpConnector.getInputSource(fileURL); + this.delimiter = delimiter; } protected void write(final Object p) { diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java index 5ce0a681cf..a13d9b791a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/project/utils/ReadExcel.java @@ -31,7 +31,7 @@ public class ReadExcel implements Closeable { final ArgumentApplicationParser parser = new ArgumentApplicationParser( IOUtils .toString( - ReadCSV.class + ReadExcel.class .getResourceAsStream( "/eu/dnetlib/dhp/actionmanager/project/parameters.json"))); diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json index b6c9c94b94..9ccb70a9f9 100644 --- a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/project/parameters.json @@ -28,6 +28,11 @@ "paramLongName" : "sheetName", "paramDescription" : "the name of the sheet in case the file is excel", "paramRequired" : false +}, { + "paramName": "d", + "paramLongName" : "delimiter", + "paramDescription" : "the delimiter between fields in case it is not ;", + "paramRequired" : false } diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index f496ea9a29..ea8832754d 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -82,7 +82,12 @@ org.apache.commons commons-text - + + eu.dnetlib.dhp + dhp-aggregation + 1.2.4-SNAPSHOT + compile + diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/GetCSV.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/GetCSV.java new file mode 100644 index 0000000000..00b6b184ba --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/GetCSV.java @@ -0,0 +1,37 @@ + +package eu.dnetlib.doiboost; + +import org.apache.commons.io.IOUtils; +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +import eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV; +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class GetCSV { + private static final Log log = LogFactory.getLog(eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV.class); + + public static void main(final String[] args) throws Exception { + final ArgumentApplicationParser parser = new ArgumentApplicationParser( + IOUtils + .toString( + GetCSV.class + .getResourceAsStream( + "/eu/dnetlib/dhp/doiboost/download_unibi_issn_gold_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"); + + try (final ReadCSV readCSV = new ReadCSV(hdfsPath, hdfsNameNode, fileURL, ',')) { + + log.info("Getting CSV file..."); + readCSV.execute(classForName); + + } + } + +} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/UnibiGoldModel.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/UnibiGoldModel.java new file mode 100644 index 0000000000..e5bd49adae --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/UnibiGoldModel.java @@ -0,0 +1,151 @@ + +package eu.dnetlib.doiboost; + +import java.io.Serializable; + +public class UnibiGoldModel implements Serializable { + private String ISSN; + private String ISSN_L; + private String ISSN_IN_DOAJ; + private String ISSN_IN_ROAD; + private String ISSN_IN_PMC; + private String ISSN_IN_OAPC; + private String ISSN_IN_WOS; + private String ISSN_IN_SCOPUS; + private String JOURNAL_IN_DOAJ; + private String JOURNAL_IN_ROAD; + private String JOURNAL_IN_PMC; + private String JOURNAL_IN_OAPC; + private String JOURNAL_IN_WOS; + private String JOURNAL_IN_SCOPUS; + private String TITLE; + 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 void setISSN_L(String ISSN_L) { + this.ISSN_L = ISSN_L; + } + + public String getISSN_IN_DOAJ() { + return ISSN_IN_DOAJ; + } + + public void setISSN_IN_DOAJ(String ISSN_IN_DOAJ) { + this.ISSN_IN_DOAJ = ISSN_IN_DOAJ; + } + + public String getISSN_IN_ROAD() { + return ISSN_IN_ROAD; + } + + public void setISSN_IN_ROAD(String ISSN_IN_ROAD) { + this.ISSN_IN_ROAD = ISSN_IN_ROAD; + } + + public String getISSN_IN_PMC() { + return ISSN_IN_PMC; + } + + public void setISSN_IN_PMC(String ISSN_IN_PMC) { + this.ISSN_IN_PMC = ISSN_IN_PMC; + } + + public String getISSN_IN_OAPC() { + return ISSN_IN_OAPC; + } + + public void setISSN_IN_OAPC(String ISSN_IN_OAPC) { + this.ISSN_IN_OAPC = ISSN_IN_OAPC; + } + + public String getISSN_IN_WOS() { + return ISSN_IN_WOS; + } + + public void setISSN_IN_WOS(String ISSN_IN_WOS) { + this.ISSN_IN_WOS = ISSN_IN_WOS; + } + + public String getISSN_IN_SCOPUS() { + return ISSN_IN_SCOPUS; + } + + public void setISSN_IN_SCOPUS(String ISSN_IN_SCOPUS) { + this.ISSN_IN_SCOPUS = ISSN_IN_SCOPUS; + } + + public String getJOURNAL_IN_DOAJ() { + return JOURNAL_IN_DOAJ; + } + + public void setJOURNAL_IN_DOAJ(String JOURNAL_IN_DOAJ) { + this.JOURNAL_IN_DOAJ = JOURNAL_IN_DOAJ; + } + + public String getJOURNAL_IN_ROAD() { + return JOURNAL_IN_ROAD; + } + + public void setJOURNAL_IN_ROAD(String JOURNAL_IN_ROAD) { + this.JOURNAL_IN_ROAD = JOURNAL_IN_ROAD; + } + + public String getJOURNAL_IN_PMC() { + return JOURNAL_IN_PMC; + } + + public void setJOURNAL_IN_PMC(String JOURNAL_IN_PMC) { + this.JOURNAL_IN_PMC = JOURNAL_IN_PMC; + } + + public String getJOURNAL_IN_OAPC() { + return JOURNAL_IN_OAPC; + } + + public void setJOURNAL_IN_OAPC(String JOURNAL_IN_OAPC) { + this.JOURNAL_IN_OAPC = JOURNAL_IN_OAPC; + } + + public String getJOURNAL_IN_WOS() { + return JOURNAL_IN_WOS; + } + + public void setJOURNAL_IN_WOS(String JOURNAL_IN_WOS) { + this.JOURNAL_IN_WOS = JOURNAL_IN_WOS; + } + + public String getJOURNAL_IN_SCOPUS() { + return JOURNAL_IN_SCOPUS; + } + + public void setJOURNAL_IN_SCOPUS(String JOURNAL_IN_SCOPUS) { + this.JOURNAL_IN_SCOPUS = JOURNAL_IN_SCOPUS; + } + + 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-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_unibi_issn_gold_parameters.json b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_unibi_issn_gold_parameters.json new file mode 100644 index 0000000000..9ccb70a9f9 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/main/resources/eu/dnetlib/dhp/doiboost/download_unibi_issn_gold_parameters.json @@ -0,0 +1,39 @@ +[ + + { + "paramName": "fu", + "paramLongName" : "fileURL", + "paramDescription" : "the url of the file to download", + "paramRequired" : true + }, + { + "paramName": "hp", + "paramLongName" : "hdfsPath", + "paramDescription" : "where to save the file", + "paramRequired" : true + }, + { + "paramName": "hnn", + "paramLongName" : "hdfsNameNode", + "paramDescription" : "the name node", + "paramRequired" : true + }, + { + "paramName": "cfn", + "paramLongName" : "classForName", + "paramDescription" : "the name of the class to deserialize the csv to", + "paramRequired" : true +}, { + "paramName": "sn", + "paramLongName" : "sheetName", + "paramDescription" : "the name of the sheet in case the file is excel", + "paramRequired" : false +}, { + "paramName": "d", + "paramLongName" : "delimiter", + "paramDescription" : "the delimiter between fields in case it is not ;", + "paramRequired" : false +} + + +] \ No newline at end of file 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 52f958d4d9..4de1a21854 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 @@ -63,6 +63,7 @@ + ${wf:conf('resumeFrom') eq 'DownloadGoldIssn'} ${wf:conf('resumeFrom') eq 'UnpackCrossrefEntries'} ${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'} ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} @@ -76,6 +77,19 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + eu.dnetlib.doiboost.GetCSV + --hdfsNameNode${nameNode} + --fileURL${unibiGoldIssnFileURL} + --hdfsPath${hdfsPath} + --classForNameeu.dnetlib.doiboost.UnibiGoldModel + + + + + + ${jobTracker} diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/GetCSVTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/GetCSVTest.java new file mode 100644 index 0000000000..6cfc90736e --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/GetCSVTest.java @@ -0,0 +1,43 @@ + +package eu.dnetlib.dhp.doiboost; + +import java.util.List; + +import org.apache.commons.io.IOUtils; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Test; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.actionmanager.project.utils.CSVParser; + +public class GetCSVTest { + + @Test + public void readUnibiGoldTest() throws Exception { + + String programmecsv = IOUtils + .toString( + getClass() + .getClassLoader() + .getResourceAsStream("eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv")); + + CSVParser csvParser = new CSVParser(); + + List pl = csvParser.parse(programmecsv, "eu.dnetlib.doiboost.UnibiGoldModel", ','); + + Assertions.assertEquals(72, pl.size()); + +// ObjectMapper OBJECT_MAPPER = new ObjectMapper(); +// +// pl.forEach(res -> { +// try { +// System.out.println(OBJECT_MAPPER.writeValueAsString(res)); +// } catch (JsonProcessingException e) { +// e.printStackTrace(); +// } +// }); + + } +} 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 new file mode 100644 index 0000000000..6d4b6cdcbd --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv @@ -0,0 +1,73 @@ +"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" +"0003-424X","0003-424X",0,1,0,0,1,0,0,1,0,0,1,0,"Annales de zootechnie.","ROAD" +"0003-4827","0003-4827",0,1,0,0,0,1,0,1,0,0,0,1,"Annals of Iowa.","ROAD" +"0004-0592","0004-0592",1,1,0,0,1,1,1,1,0,0,1,1,"Archivos de Zootecnia","DOAJ" +"0004-282X","0004-282X",1,1,0,0,1,1,1,1,0,0,1,1,"Arquivos de Neuro-Psiquiatria","DOAJ" +"0006-3096","0006-3096",0,1,0,0,0,0,0,1,0,0,0,0,"Biologia.","ROAD" +"0006-8705","0006-8705",1,1,0,0,1,1,1,1,0,0,1,1,"Bragantia","DOAJ" +"0007-5124","0007-5124",0,1,0,0,1,0,0,1,1,0,1,1,"Experimental animals.","ROAD" +"0007-9502","0007-9502",0,1,0,0,0,0,0,1,0,0,0,0,"Caesaraugusta.","ROAD" +"0008-7386","0008-7386",1,1,0,0,0,1,1,1,0,0,0,1,"Časopis pro Moderní Filologii","DOAJ" +"0008-7629","0008-7629",1,0,0,0,0,0,1,0,0,0,0,0,"Catalogue and Index","DOAJ" +"0015-573X","0015-573X",0,1,0,0,0,0,0,1,0,0,0,0,"Folia quaternaria.","ROAD" +"0016-6987","0016-6987",1,0,0,0,1,1,1,0,0,0,1,1,"Genus","DOAJ" +"0016-7789","0016-7789",1,1,0,0,0,1,1,1,0,0,0,1,"Geologija ","DOAJ" +"0021-5007","0021-5007",0,1,0,0,0,1,0,1,0,0,0,1,"Nihon Seitai Gakkaishi.","ROAD" +"0023-4001","0023-4001",0,1,0,0,1,1,0,1,0,0,1,1,"Korean Journal of Parasitology","ROAD" +"0023-5415","0023-5415",1,1,0,0,0,0,1,1,0,0,0,0,"Kunst og Kultur","DOAJ" +"0026-1165","0026-1165",1,0,0,0,1,1,1,0,0,0,1,1,"Journal of the Meteorological Society of Japan","DOAJ" +"0029-0181","0029-0181",0,1,0,0,0,0,0,1,0,0,0,0,"Nihon butsuri gakkaishi.","ROAD" +"0034-7000","0034-7000",1,1,0,0,0,1,1,1,0,0,0,1,"Revista Argentina de Cardiología","DOAJ" +"0034-7523","0034-7523",0,1,0,0,0,1,0,1,0,0,0,1,"Revista cubana de medicina.","ROAD" +"0034-8244","0034-8244",1,0,0,0,1,1,1,0,0,0,1,1,"Revista de Filosofia","DOAJ" +"0034-8678","0034-8678",1,0,0,0,0,0,1,0,0,0,0,0,"Revista de Pedagogie","DOAJ" +"0036-8709","0036-8709",1,1,1,0,1,1,1,1,1,0,1,1,"Scientia Pharmaceutica","DOAJ" +"0044-4855","0044-4855",0,1,0,0,0,0,0,1,0,0,0,0,"Život i škola.","ROAD" +"0048-7449","0048-7449",1,1,0,0,1,1,1,1,0,0,1,1,"Reumatismo","DOAJ" +"0048-766X","0048-766X",0,1,0,0,0,1,0,1,0,0,0,1,"Revista chilena de obstetricia y ginecología.","ROAD" +"0065-1400","0065-1400",0,1,0,0,1,1,0,1,0,0,1,1,"Acta Neurobiologiae Experimentalis.","ROAD" +"0066-6742","0066-6742",1,0,0,0,1,1,1,0,0,0,1,1,"Archivo Español de Arqueología","DOAJ" +"0073-2435","0073-2435",1,1,0,0,1,1,1,1,0,0,1,1,"Historia (Santiago)","DOAJ" +"0073-4918","0073-4918",0,1,0,0,0,0,0,1,0,0,0,0,"Illinois Natural History Survey bulletin.","ROAD" +"0075-7411","0075-7411",1,0,0,0,0,0,1,0,0,0,0,0,"Anales","DOAJ" +"0077-2704","0077-2704",0,1,0,0,0,0,0,1,0,0,0,0,"Namn och bygd.","ROAD" +"0078-5466","0078-5466",0,1,0,0,1,1,0,1,0,0,1,1,"Optica Applicata.","ROAD" +"0079-4929","0079-4929",1,1,0,0,0,0,1,1,0,0,0,0,"Právněhistorické studie","DOAJ" +"0100-3283","0100-3283",0,1,0,0,0,0,0,1,0,0,0,0,"Hansenologia Internationalis.","ROAD" +"0100-4042","0100-4042",1,1,0,0,1,1,1,1,0,0,1,1,"Química Nova","DOAJ" +"0100-8692","0100-8692",1,1,0,0,1,0,1,1,0,0,1,1,"Arquivos Brasileiros de Psicologia ","DOAJ" +"0102-4469","0102-4469",1,0,0,0,0,0,1,0,0,0,0,0,"Perspectiva Teológica","DOAJ" +"0102-6992","0102-6992",1,1,0,0,0,1,1,1,0,0,0,1,"Sociedade e Estado","DOAJ" +"0103-1570","0103-1570",1,1,0,0,0,0,1,1,0,0,0,0,"Revista Sociedade & Natureza","DOAJ" +"0103-2070","0103-2070",1,1,0,0,1,1,1,1,0,0,1,1,"Tempo Social","DOAJ" +"0104-0588","0104-0588",1,1,0,0,1,0,1,1,0,0,1,0,"Revista de Estudos da Linguagem","DOAJ" +"0104-6497","0104-6497",1,1,0,0,1,0,1,1,0,0,1,0,"Nauplius","DOAJ" +"0104-8929","0104-8929",0,1,0,0,0,0,0,1,0,0,0,0,"Saeculum.","ROAD" +"0104-9496","0104-9496",1,0,0,0,0,0,1,0,0,0,0,0,"Revista do Direito","DOAJ" +"0120-0380","0120-0380",0,1,0,0,1,0,0,1,0,0,1,0,"Boletín de matemáticas.","ROAD" +"0120-100X","0120-100X",1,1,0,0,0,0,1,1,0,0,0,0,"Revista Ion","DOAJ" +"0120-4807","0120-4807",1,1,0,0,0,0,1,1,0,0,0,0,"Universitas Humanística","DOAJ" +"0121-4004","0121-4004",1,0,0,0,1,1,1,0,0,0,1,1,"Vitae","DOAJ" +"0121-4500","0121-4500",1,1,0,0,0,0,1,1,0,0,0,0,"Avances en Enfermería","DOAJ" +"0121-8697","0121-8697",1,0,0,0,0,0,1,0,0,0,0,0,"Revista de Derecho","DOAJ" +"0122-5197","0122-5197",0,1,0,0,0,1,0,1,0,0,0,1,"Memoria y Sociedad.","ROAD" +"0161-0457","0161-0457",1,0,1,1,1,1,1,0,1,1,1,1,"Scanning","DOAJ" +"0215-4706","0215-4706",1,1,0,0,0,0,1,1,0,0,0,0,"Floribunda.","ROAD" +"0324-6000","0324-6000",0,1,0,0,1,1,0,1,0,0,1,1,"Periodica polytechnica. Electrical engineering","ROAD" +"0325-187X","0325-187X",1,1,0,0,0,1,1,1,0,0,0,1,"Meteorologica","DOAJ" +"0326-7237","0326-7237",1,1,0,0,0,1,1,1,0,0,0,1,"Geoacta.","ROAD" +"0327-1676","0327-1676",0,1,0,0,0,0,1,1,0,0,0,0,"Andes","DOAJ" +"0327-2818","0327-2818",1,0,0,0,0,0,1,0,0,0,0,0,"Dominguezia","DOAJ" +"0327-5108","0327-5108",1,0,0,0,0,0,1,0,0,0,0,0,"Páginas de Filosofía","DOAJ" +"0327-585X","0327-585X",1,1,0,0,0,0,1,1,0,0,0,0,"Actualidad Económica","DOAJ" +"0327-6147","0327-6147",0,1,0,0,0,0,0,1,0,0,0,0,"Papeles de trabajo.","ROAD" +"0327-7763","0327-7763",0,1,0,0,0,0,0,1,0,0,0,0,"Revista del IICE.","ROAD" +"0327-9286","0327-9286",1,1,0,0,0,0,1,1,0,0,0,0,"Acta Toxicológica Argentina","DOAJ" +"0328-1205","0328-1205",1,1,0,0,1,1,1,1,0,0,1,1,"Synthesis (La Plata)","DOAJ" +"0329-5893","0329-5893",0,1,0,0,0,0,0,1,0,0,0,0,"Investigaciones en psicología..","ROAD" +"0329-8213","0329-8213",1,0,0,0,0,0,1,0,0,0,0,0,"Historia Regional","DOAJ" +"0332-5024","0332-5024",1,1,0,0,0,0,1,1,0,0,0,0,"Studia Musicologica Norvegica","DOAJ" +"0350-185X","0350-185X",1,1,0,0,0,0,1,1,0,0,0,0,"Južnoslovenski Filolog","DOAJ" diff --git a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java index a985d23718..2c82402900 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java +++ b/dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java @@ -16,7 +16,6 @@ import javax.xml.transform.*; import javax.xml.transform.dom.DOMSource; import javax.xml.transform.stream.StreamResult; -import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; import org.apache.commons.lang3.StringUtils; import org.apache.spark.util.LongAccumulator; import org.dom4j.Document; @@ -43,6 +42,7 @@ 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.Result; +import eu.dnetlib.dhp.schema.oaf.utils.IdentifierFactory; public class XmlRecordFactory implements Serializable { From eb07f7f40f76b9a9c0a3f72549908c4432779558 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 27 Jul 2021 12:27:26 +0200 Subject: [PATCH 02/51] Hosted By Map --- .../eu/dnetlib/dhp/transform/terms.txt | 2 +- .../eu/dnetlib/dhp/transform/input_itgv4.xml | 2 +- ...c_cleaning_OPENAIREplus_compliant_hal_orig | 6 +- ...e_datacite_ExchangeLandingpagePid_orig.xsl | 20 +-- ...enaire_datacite_ExchangeLandingpagePid.xsl | 14 +- .../eu/dnetlib/dhp/transform/terms.txt | 2 +- .../crossref_mapping.csv | 4 +- .../dhp/doiboost/issn_gold_oa_version_4.csv | 2 +- dhp-workflows/dhp-graph-mapper/pom.xml | 5 + .../dhp/oa/graph/hostebymap/Aggregators.scala | 54 ++++++ .../dhp/oa/graph/hostebymap/Constants.java | 15 ++ .../dhp/oa/graph/hostebymap/GetCSV.java | 111 ++++++++++++ .../SparkPrepareHostedByMapData.scala | 158 ++++++++++++++++++ .../oa/graph/hostebymap/model/DOAJModel.java | 53 ++++++ .../hostebymap/model/UnibiGoldModel.java | 44 +++++ .../oa/graph/hostedbymap/TestPreprocess.scala | 59 +++++++ .../dhp/oa/graph/hostedbymap/TestReadCSV.java | 111 ++++++++++++ .../eu/dnetlib/dhp/oa/graph/clean/terms.txt | 2 +- .../dhp/oa/graph/hostedbymap/datasource.json | 10 ++ .../graph/hostedbymap/doaj_transformed.json | 25 +++ .../dhp/oa/graph/hostedbymap/unibiGold.csv | 37 ++++ .../graph/hostedbymap/unibi_transformed.json | 29 ++++ .../dhp/oa/graph/raw/oaf_claim_dedup.xml | 4 +- .../dhp/sx/graph/bio/pubmed/pubmed.xml | 46 ++--- .../eu/dnetlib/dhp/transform/terms.txt | 2 +- 25 files changed, 764 insertions(+), 53 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Aggregators.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Constants.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/GetCSV.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/SparkPrepareHostedByMapData.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/DOAJModel.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/UnibiGoldModel.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPreprocess.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestReadCSV.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasource.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doaj_transformed.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibiGold.csv create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibi_transformed.json 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/doaj_transformed.json @@ -0,0 +1,25 @@ +{"journalTitle":"Lëd i Sneg","issn":"2076-6734","eissn":"2412-3765","reviewProcess":"Double blind peer review"} +{"journalTitle":"Компьютерные исследования и моделирование","issn":"2076-7633","eissn":"2077-6853","reviewProcess":"Blind peer review"} +{"journalTitle":" Историко-биологические исследования","issn":"2076-8176","eissn":"2500-1221","reviewProcess":"Double blind peer review"} +{"journalTitle":"Інформаційні технології і засоби навчання","issn":"2076-8184","eissn":"","reviewProcess":"Double blind peer review"} +{"journalTitle":"Revue Internationale de Pédagogie de l’Enseignement Supérieur","issn":"","eissn":"2076-8427","reviewProcess":"Double blind peer review"} +{"journalTitle":"Проблемы развития территории","issn":"2076-8915","eissn":"2409-9007","reviewProcess":"Double blind peer review"} +{"journalTitle":"Rambam Maimonides Medical Journal","issn":"","eissn":"2076-9172","reviewProcess":"Peer review"} +{"journalTitle":"Membranes","issn":"2077-0375","eissn":"","reviewProcess":"Blind peer review"} +{"journalTitle":"Journal of Clinical Medicine","issn":"","eissn":"2077-0383","reviewProcess":"Blind peer review"} +{"journalTitle":"Agriculture","issn":"","eissn":"2077-0472","reviewProcess":"Blind peer review"} +{"journalTitle":"Standartnye Obrazcy","issn":"2077-1177","eissn":"","reviewProcess":"Double blind peer review"} +{"journalTitle":"Металл и литье Украины","issn":"2077-1304","eissn":"2706-5529","reviewProcess":"Double blind peer review"} +{"journalTitle":"Journal of Marine Science and Engineering","issn":"","eissn":"2077-1312","reviewProcess":"Blind peer review"} +{"journalTitle":"Religions","issn":"","eissn":"2077-1444","reviewProcess":"Double blind peer review"} +{"journalTitle":"GW-Unterricht","issn":"2077-1517","eissn":"2414-4169","reviewProcess":"Double blind peer review"} +{"journalTitle":"UCV-Scientia","issn":"2077-172X","eissn":"","reviewProcess":"Peer review"} +{"journalTitle":"Sovremennye Issledovaniâ Socialʹnyh Problem","issn":"2077-1770","eissn":"2218-7405","reviewProcess":"Double blind peer review"} +{"journalTitle":"Granì","issn":"2077-1800","eissn":"2413-8738","reviewProcess":"Double blind peer review"} +{"journalTitle":"Journal of Economics Finance and Administrative Science","issn":"2077-1886","eissn":"2218-0648","reviewProcess":"Double blind peer review"} +{"journalTitle":"Science Education International","issn":"","eissn":"2077-2327","reviewProcess":"Double blind peer review"} +{"journalTitle":"Edumecentro","issn":"","eissn":"2077-2874","reviewProcess":"Double blind peer review"} +{"journalTitle":"Monteverdia","issn":"","eissn":"2077-2890","reviewProcess":"Double blind peer review"} +{"journalTitle":"Transformación","issn":"","eissn":"2077-2955","reviewProcess":"Double blind peer review"} +{"journalTitle":"Journal of Space Technology","issn":"2077-3099","eissn":"2411-5029","reviewProcess":"Double blind peer review"} +{"journalTitle":"Revue de Primatologie","issn":"","eissn":"2077-3757","reviewProcess":"Peer review"} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibiGold.csv b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibiGold.csv new file mode 100644 index 0000000000..eb5d93451a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibiGold.csv @@ -0,0 +1,37 @@ +"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" +"0003-424X","0003-424X",0,1,0,0,1,0,0,1,0,0,1,0,"Annales de zootechnie.","ROAD" +"0003-4827","0003-4827",0,1,0,0,0,1,0,1,0,0,0,1,"Annals of Iowa.","ROAD" +"0004-0592","0004-0592",1,1,0,0,1,1,1,1,0,0,1,1,"Archivos de Zootecnia","DOAJ" +"0004-282X","0004-282X",1,1,0,0,1,1,1,1,0,0,1,1,"Arquivos de Neuro-Psiquiatria","DOAJ" +"0006-3096","0006-3096",0,1,0,0,0,0,0,1,0,0,0,0,"Biologia.","ROAD" +"0006-8705","0006-8705",1,1,0,0,1,1,1,1,0,0,1,1,"Bragantia","DOAJ" +"0007-5124","0007-5124",0,1,0,0,1,0,0,1,1,0,1,1,"Experimental animals.","ROAD" +"0007-9502","0007-9502",0,1,0,0,0,0,0,1,0,0,0,0,"Caesaraugusta.","ROAD" +"0008-7386","0008-7386",1,1,0,0,0,1,1,1,0,0,0,1,"Časopis pro Moderní Filologii","DOAJ" +"0008-7629","0008-7629",1,0,0,0,0,0,1,0,0,0,0,0,"Catalogue and Index","DOAJ" +"0015-573X","0015-573X",0,1,0,0,0,0,0,1,0,0,0,0,"Folia quaternaria.","ROAD" +"0016-6987","0016-6987",1,0,0,0,1,1,1,0,0,0,1,1,"Genus","DOAJ" +"0016-7789","0016-7789",1,1,0,0,0,1,1,1,0,0,0,1,"Geologija ","DOAJ" +"0021-5007","0021-5007",0,1,0,0,0,1,0,1,0,0,0,1,"Nihon Seitai Gakkaishi.","ROAD" +"0023-4001","0023-4001",0,1,0,0,1,1,0,1,0,0,1,1,"Korean Journal of Parasitology","ROAD" +"0023-5415","0023-5415",1,1,0,0,0,0,1,1,0,0,0,0,"Kunst og Kultur","DOAJ" +"0026-1165","0026-1165",1,0,0,0,1,1,1,0,0,0,1,1,"Journal of the Meteorological Society of Japan","DOAJ" +"0029-0181","0029-0181",0,1,0,0,0,0,0,1,0,0,0,0,"Nihon butsuri gakkaishi.","ROAD" +"0034-7000","0034-7000",1,1,0,0,0,1,1,1,0,0,0,1,"Revista Argentina de Cardiología","DOAJ" +"0034-7523","0034-7523",0,1,0,0,0,1,0,1,0,0,0,1,"Revista cubana de medicina.","ROAD" +"0034-8244","0034-8244",1,0,0,0,1,1,1,0,0,0,1,1,"Revista de Filosofia","DOAJ" +"0034-8678","0034-8678",1,0,0,0,0,0,1,0,0,0,0,0,"Revista de Pedagogie","DOAJ" +"0036-8709","0036-8709",1,1,1,0,1,1,1,1,1,0,1,1,"Scientia Pharmaceutica","DOAJ" +"0044-4855","0044-4855",0,1,0,0,0,0,0,1,0,0,0,0,"Život i škola.","ROAD" +"0048-7449","0048-7449",1,1,0,0,1,1,1,1,0,0,1,1,"Reumatismo","DOAJ" +"0048-766X","0048-766X",0,1,0,0,0,1,0,1,0,0,0,1,"Revista chilena de obstetricia y ginecología.","ROAD" +"0065-1400","0065-1400",0,1,0,0,1,1,0,1,0,0,1,1,"Acta Neurobiologiae Experimentalis.","ROAD" +"0066-6742","0066-6742",1,0,0,0,1,1,1,0,0,0,1,1,"Archivo Español de Arqueología","DOAJ" +"0073-2435","0073-2435",1,1,0,0,1,1,1,1,0,0,1,1,"Historia (Santiago)","DOAJ" +"0073-4918","0073-4918",0,1,0,0,0,0,0,1,0,0,0,0,"Illinois Natural History Survey bulletin.","ROAD" +"0075-7411","0075-7411",1,0,0,0,0,0,1,0,0,0,0,0,"Anales","DOAJ" +"0077-2704","0077-2704",0,1,0,0,0,0,0,1,0,0,0,0,"Namn och bygd.","ROAD" +"0078-5466","0078-5466",0,1,0,0,1,1,0,1,0,0,1,1,"Optica Applicata.","ROAD" \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibi_transformed.json 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 From 0424f47494ffcc792fc4d9c7dc4e79407dc105c5 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 28 Jul 2021 10:24:13 +0200 Subject: [PATCH 03/51] HostedByMap fixing issues --- .../dhp/oa/graph/hostebymap/Aggregators.scala | 2 +- .../SparkPrepareHostedByMapData.scala | 240 +++++++++++------- .../oa/graph/hostedbymap/TestPreprocess.scala | 85 ++++++- .../dhp/oa/graph/hostedbymap/datasource.json | 20 +- 4 files changed, 234 insertions(+), 113 deletions(-) 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 index d984183399..561d2bbf45 100644 --- 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 @@ -5,7 +5,7 @@ import org.apache.spark.sql.expressions.Aggregator case class HostedByItemType(id: String, officialname: String, issn: String, eissn: String, lissn: String, openAccess: Boolean) {} - +case class HostedByInfo(id: String, officialname: String, journal_id: String, provenance : String, id_type: String) {} object Aggregators { 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 index 55b6e36cd0..b66e972818 100644 --- 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 @@ -2,27 +2,23 @@ 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 eu.dnetlib.dhp.schema.oaf.{Datasource} 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 +import com.fasterxml.jackson.databind.ObjectMapper 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 = { @@ -32,59 +28,144 @@ object SparkPrepareHostedByMapData { 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) + case Constants.ISSN => HostedByItemType(openaire.id, openaire.officialname, openaire.journal_id, "", "", isOpenAccess) + case Constants.EISSN => HostedByItemType(openaire.id, openaire.officialname, "", openaire.journal_id, "", isOpenAccess) + case Constants.ISSNL => HostedByItemType(openaire.id, openaire.officialname, "", "", openaire.journal_id, isOpenAccess) // catch the default with a variable so you can print it - case whoa => return null + case whoa => null } } - def toHostedByMap(input: HostedByItemType): ListBuffer[String] = { - implicit val formats = DefaultFormats - val serializedJSON:String = write(input) +// 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 +// +// } - var hostedBy = new ListBuffer[String]() + def getHostedByItemType(id:String, officialname: String, issn:String, eissn:String, issnl:String, oa:Boolean): HostedByItemType = { + if(issn != null){ + if(eissn != null){ + if(issnl != null){ + HostedByItemType(id, officialname, issn, eissn, issnl , oa) + }else{ + HostedByItemType(id, officialname, issn, eissn, "" , oa) + } + }else{ + if(issnl != null){ + HostedByItemType(id, officialname, issn, "", issnl , oa) + }else{ + HostedByItemType(id, officialname, issn, "", "" , oa) + } + } + }else{ + if(eissn != null){ + if(issnl != null){ + HostedByItemType(id, officialname, "", eissn, issnl , oa) + }else{ + HostedByItemType(id, officialname, "", eissn, "" , oa) + } + }else{ + if(issnl != null){ + HostedByItemType(id, officialname, "", "", issnl , oa) + }else{ + HostedByItemType("", "", "", "", "" , oa) + } + } + } + } + + def oaToHostedbyItemType(dats: Datasource): HostedByItemType = { + if (dats.getJournal != null) { + + return getHostedByItemType(dats.getId, dats.getOfficialname.getValue, dats.getJournal.getIssnPrinted, dats.getJournal.getIssnOnline, dats.getJournal.getIssnLinking, false) + } + HostedByItemType("","","","","",false) + } + + def oaHostedByDataset(spark:SparkSession, datasourcePath : String) : Dataset[HostedByItemType] = { + + import spark.implicits._ + + + val mapper = new ObjectMapper() + + implicit var encoderD = Encoders.kryo[Datasource] + + val dd : Dataset[Datasource] = spark.read.textFile(datasourcePath) + .map(r => mapper.readValue(r, classOf[Datasource])) + + dd.map{ddt => oaToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals(""))) + + } + + + def goldToHostedbyItemType(gold: UnibiGoldModel): HostedByItemType = { + return getHostedByItemType(Constants.UNIBI, gold.getTitle, gold.getIssn, "", gold.getIssn_l, true) + } + + + def goldHostedByDataset(spark:SparkSession, datasourcePath:String) : Dataset[HostedByItemType] = { + import spark.implicits._ + + implicit val mapEncoderUnibi: Encoder[UnibiGoldModel] = Encoders.kryo[UnibiGoldModel] + + val mapper = new ObjectMapper() + + val dd : Dataset[UnibiGoldModel] = spark.read.textFile(datasourcePath) + .map(r => mapper.readValue(r, classOf[UnibiGoldModel])) + + dd.map{ddt => goldToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals(""))) + + } + + def doajToHostedbyItemType(doaj: DOAJModel): HostedByItemType = { + + return getHostedByItemType(Constants.DOAJ, doaj.getJournalTitle, doaj.getIssn, doaj.getEissn, "", true) + } + + def doajHostedByDataset(spark:SparkSession, datasourcePath:String) : Dataset[HostedByItemType] = { + import spark.implicits._ + + implicit val mapEncoderDOAJ: Encoder[DOAJModel] = Encoders.kryo[DOAJModel] + + val mapper = new ObjectMapper() + + val dd : Dataset[DOAJModel] = spark.read.textFile(datasourcePath) + .map(r => mapper.readValue(r, classOf[DOAJModel])) + + dd.map{ddt => doajToHostedbyItemType(ddt)}.filter(hb => !(hb.id.equals(""))) + + } + + def toList(input: HostedByItemType): List[(String, HostedByItemType)] = { + var lst : List[(String, HostedByItemType)] = List() if(!input.issn.equals("")){ - hostedBy += "{\"" + input.issn + "\":" + serializedJSON + "}" + lst = (input.issn, input) :: lst } if(!input.eissn.equals("")){ - hostedBy += "{\"" + input.eissn + "\":" + serializedJSON + "}" + lst = (input.eissn, input) :: lst } if(!input.lissn.equals("")){ - hostedBy += "{\"" + input.lissn + "\":" + serializedJSON + "}" + lst = (input.lissn, input) :: lst } - - hostedBy - + lst } - 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) @@ -105,53 +186,34 @@ object SparkPrepareHostedByMapData { + implicit val formats = DefaultFormats + 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 doajDataset: Dataset[DOAJModel] = spark.read.textFile(workingDirPath + "/doaj").as[DOAJModel] - 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") + val dats : Dataset[HostedByItemType] = + oaHostedByDataset(spark, datasourcePath) + .union(goldHostedByDataset(spark, workingDirPath + "/unibi_gold")) + .union(doajHostedByDataset(spark, workingDirPath + "/doaj")) + dats.flatMap(hbi => toList(hbi)) + .groupByKey(_._1) +// +// + +// + +// +// Aggregators.createHostedByItemTypes(oa.joinWith(doaj, oa.col("journal_id").equalTo(doaj.col("journal_id")), "left") +// .joinWith(gold, $"_1.col('journal_id')".equalTo(gold.col("journal_id")), "left").map(toHostedByItemType) +// .filter(i => i != null)) +// .flatMap(toHostedByMap) +// .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/HostedByMap") +// +// } 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 index 657f20fce4..8e5657bfc1 100644 --- 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 @@ -2,22 +2,23 @@ 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 com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.oa.graph.hostebymap.{Constants, HostedByInfo, SparkPrepareHostedByMapData} +import eu.dnetlib.dhp.schema.oaf.Datasource import org.apache.spark.SparkConf -import org.apache.spark.sql.{Dataset, SparkSession} -import org.codehaus.jackson.map.ObjectMapper +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} 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.collection.mutable.ListBuffer import scala.io.Source -class TestPreprocess { +class TestPreprocess extends java.io.Serializable{ - val logger: Logger = LoggerFactory.getLogger(getClass) - val mapper = new ObjectMapper() + implicit val mapEncoderDats: Encoder[Datasource] = Encoders.kryo[Datasource] + implicit val schema = Encoders.product[HostedByInfo] @@ -27,7 +28,11 @@ class TestPreprocess { import org.apache.spark.sql.Encoders implicit val formats = DefaultFormats - import org.json4s.jackson.Serialization.write + + val logger: Logger = LoggerFactory.getLogger(getClass) + val mapper = new ObjectMapper() + + val conf = new SparkConf() conf.setMaster("local[*]") @@ -41,12 +46,67 @@ class TestPreprocess { val path = getClass.getResource("datasource.json").getPath - val schema = Encoders.product[HostedByInfo] + println(SparkPrepareHostedByMapData.oaHostedByDataset(spark, path).count) - spark.read.textFile(path).foreach(r => println(mapper.writeValueAsString(r))) -// SparkPrepareHostedByMapData.readOADataset(path, spark) -// .foreach(r => println(write(r))) + + spark.close() + } + + + @Test + def readGold():Unit = { + + implicit val formats = DefaultFormats + + val logger: Logger = LoggerFactory.getLogger(getClass) + val mapper = new ObjectMapper() + + + + 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("unibi_transformed.json").getPath + + + println(SparkPrepareHostedByMapData.goldHostedByDataset(spark, path).count) + + + + spark.close() + } + + @Test + def readDoaj():Unit = { + + implicit val formats = DefaultFormats + + val logger: Logger = LoggerFactory.getLogger(getClass) + val mapper = new ObjectMapper() + + + + 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("doaj_transformed.json").getPath + + + println(SparkPrepareHostedByMapData.doajHostedByDataset(spark, path).count) + spark.close() @@ -55,5 +115,4 @@ class TestPreprocess { - } 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 index 15e1dcc45a..818aaa7167 100644 --- 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 @@ -1,10 +1,10 @@ -{"accessinfopackage":[],"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"dataprovider":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":false},"datasourcetype":{"classid":"pubsrepository::journal","classname":"Journal","schemeid":"dnet:datasource_typologies","schemename":"dnet:datasource_typologies"},"dateofcollection":"2020-03-01","englishname":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Известия высших учебных заведений: Проблемы энергетики"},"extraInfo":[],"id":"10|doajarticles::0ab37b7620eb9a73ac95d3ca4320c97d","journal":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"issnPrinted":"1998-9903","name":"Известия высших учебных заведений: Проблемы энергетики"},"lastupdatetimestamp":1626336932282,"latitude":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0.0"},"longitude":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0.0"},"namespaceprefix":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"doaj19989903"},"odcontenttypes":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Journal articles"}],"odlanguages":[],"odnumberofitems":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"0.0"},"officialname":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"Известия высших учебных заведений: Проблемы энергетики"},"openairecompatibility":{"classid":"hostedBy","classname":"collected from a compatible aggregator","schemeid":"dnet:datasourceCompatibilityLevel","schemename":"dnet:datasourceCompatibilityLevel"},"originalId":["doajarticles::1998-9903"],"pid":[],"policies":[],"serviceprovider":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":false},"subjects":[{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"Technology: Electrical engineering. Electronics. Nuclear engineering: Production of electric energy or power. Powerplants. 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delete mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/GetCSV.java delete mode 100644 dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/UnibiGoldModel.java diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/GetCSV.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/GetCSV.java deleted file mode 100644 index 00b6b184ba..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/GetCSV.java +++ /dev/null @@ -1,37 +0,0 @@ - -package eu.dnetlib.doiboost; - -import org.apache.commons.io.IOUtils; -import org.apache.commons.logging.Log; -import org.apache.commons.logging.LogFactory; - -import eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV; -import eu.dnetlib.dhp.application.ArgumentApplicationParser; - -public class GetCSV { - private static final Log log = LogFactory.getLog(eu.dnetlib.dhp.actionmanager.project.utils.ReadCSV.class); - - public static void main(final String[] args) throws Exception { - final ArgumentApplicationParser parser = new ArgumentApplicationParser( - IOUtils - .toString( - GetCSV.class - .getResourceAsStream( - "/eu/dnetlib/dhp/doiboost/download_unibi_issn_gold_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"); - - try (final ReadCSV readCSV = new ReadCSV(hdfsPath, hdfsNameNode, fileURL, ',')) { - - log.info("Getting CSV file..."); - readCSV.execute(classForName); - - } - } - -} diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/UnibiGoldModel.java b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/UnibiGoldModel.java deleted file mode 100644 index e5bd49adae..0000000000 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/UnibiGoldModel.java +++ /dev/null @@ -1,151 +0,0 @@ - -package eu.dnetlib.doiboost; - -import java.io.Serializable; - -public class UnibiGoldModel implements Serializable { - private String ISSN; - private String ISSN_L; - private String ISSN_IN_DOAJ; - private String ISSN_IN_ROAD; - private String ISSN_IN_PMC; - private String ISSN_IN_OAPC; - private String ISSN_IN_WOS; - private String ISSN_IN_SCOPUS; - private String JOURNAL_IN_DOAJ; - private String JOURNAL_IN_ROAD; - private String JOURNAL_IN_PMC; - private String JOURNAL_IN_OAPC; - private String JOURNAL_IN_WOS; - private String JOURNAL_IN_SCOPUS; - private String TITLE; - 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 void setISSN_L(String ISSN_L) { - this.ISSN_L = ISSN_L; - } - - public String getISSN_IN_DOAJ() { - return ISSN_IN_DOAJ; - } - - public void setISSN_IN_DOAJ(String ISSN_IN_DOAJ) { - this.ISSN_IN_DOAJ = ISSN_IN_DOAJ; - } - - public String getISSN_IN_ROAD() { - return ISSN_IN_ROAD; - } - - public void setISSN_IN_ROAD(String ISSN_IN_ROAD) { - this.ISSN_IN_ROAD = ISSN_IN_ROAD; - } - - public String getISSN_IN_PMC() { - return ISSN_IN_PMC; - } - - public void setISSN_IN_PMC(String ISSN_IN_PMC) { - this.ISSN_IN_PMC = ISSN_IN_PMC; - } - - public String getISSN_IN_OAPC() { - return ISSN_IN_OAPC; - } - - public void setISSN_IN_OAPC(String ISSN_IN_OAPC) { - this.ISSN_IN_OAPC = ISSN_IN_OAPC; - } - - public String getISSN_IN_WOS() { - return ISSN_IN_WOS; - } - - public void setISSN_IN_WOS(String ISSN_IN_WOS) { - this.ISSN_IN_WOS = ISSN_IN_WOS; - } - - public String getISSN_IN_SCOPUS() { - return ISSN_IN_SCOPUS; - } - - public void setISSN_IN_SCOPUS(String ISSN_IN_SCOPUS) { - this.ISSN_IN_SCOPUS = ISSN_IN_SCOPUS; - } - - public String getJOURNAL_IN_DOAJ() { - return JOURNAL_IN_DOAJ; - } - - public void setJOURNAL_IN_DOAJ(String JOURNAL_IN_DOAJ) { - this.JOURNAL_IN_DOAJ = JOURNAL_IN_DOAJ; - } - - public String getJOURNAL_IN_ROAD() { - return JOURNAL_IN_ROAD; - } - - public void setJOURNAL_IN_ROAD(String JOURNAL_IN_ROAD) { - this.JOURNAL_IN_ROAD = JOURNAL_IN_ROAD; - } - - public String getJOURNAL_IN_PMC() { - return JOURNAL_IN_PMC; - } - - public void setJOURNAL_IN_PMC(String JOURNAL_IN_PMC) { - this.JOURNAL_IN_PMC = JOURNAL_IN_PMC; - } - - public String getJOURNAL_IN_OAPC() { - return JOURNAL_IN_OAPC; - } - - public void setJOURNAL_IN_OAPC(String JOURNAL_IN_OAPC) { - this.JOURNAL_IN_OAPC = JOURNAL_IN_OAPC; - } - - public String getJOURNAL_IN_WOS() { - return JOURNAL_IN_WOS; - } - - public void setJOURNAL_IN_WOS(String JOURNAL_IN_WOS) { - this.JOURNAL_IN_WOS = JOURNAL_IN_WOS; - } - - public String getJOURNAL_IN_SCOPUS() { - return JOURNAL_IN_SCOPUS; - } - - public void setJOURNAL_IN_SCOPUS(String JOURNAL_IN_SCOPUS) { - this.JOURNAL_IN_SCOPUS = JOURNAL_IN_SCOPUS; - } - - 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; - } -} From baad01cadcc499909d68651ff03a60213b7b8c76 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Thu, 29 Jul 2021 13:04:39 +0200 Subject: [PATCH 05/51] hostedbymap --- .../dhp/oa/dedup/GroupEntitiesSparkJob.java | 3 +- .../doiboost/DoiBoostMappingUtil.scala | 2 + .../dhp/oa/graph/hostebymap/Aggregators.scala | 54 ------ .../dhp/oa/graph/hostebymap/Constants.java | 15 -- .../dhp/oa/graph/hostebymap/GetCSV.java | 111 ------------ .../oa/graph/hostebymap/model/DOAJModel.java | 53 ------ .../hostebymap/model/UnibiGoldModel.java | 44 ----- .../oa/graph/hostedbymap/Aggregators.scala | 97 ++++++++++ .../dhp/oa/graph/hostedbymap/Constants.java | 13 ++ .../dhp/oa/graph/hostedbymap/GetCSV.java | 107 +++++++++++ .../SparkProduceHostedByMap.scala} | 107 ++++++----- .../oa/graph/hostedbymap/model/DOAJModel.java | 52 ++++++ .../hostedbymap/model/UnibiGoldModel.java | 45 +++++ .../hostedbymap/download_csv_parameters.json | 37 ++++ .../oa/graph/hostedbymap/hostedby_params.json | 38 ++++ .../hostedbymap/oozie_app/config-default.xml | 30 ++++ .../graph/hostedbymap/oozie_app/workflow.xml | 148 +++++++++++++++ .../oa/graph/hostedbymap/TestPreprocess.scala | 127 +++++++++---- .../dhp/oa/graph/hostedbymap/TestReadCSV.java | 168 +++++++++--------- .../dnetlib/dhp/oa/graph/raw/MappersTest.java | 28 +-- .../dhp/oa/graph/hostedbymap/datasource.json | 2 +- .../graph/hostedbymap/datasourceHostedByItem | 9 + .../dhp/oa/graph/hostedbymap/doajHostedByItem | 25 +++ .../oa/graph/hostedbymap/unibyHostedByItem | 29 +++ 24 files changed, 885 insertions(+), 459 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Aggregators.scala delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Constants.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/GetCSV.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/DOAJModel.java delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/UnibiGoldModel.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Constants.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/GetCSV.java rename dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/{hostebymap/SparkPrepareHostedByMapData.scala => hostedbymap/SparkProduceHostedByMap.scala} (76%) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/UnibiGoldModel.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_csv_parameters.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_params.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/config-default.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasourceHostedByItem create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doajHostedByItem create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibyHostedByItem diff --git a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/GroupEntitiesSparkJob.java b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/GroupEntitiesSparkJob.java index 3f27b94422..58009bfcfc 100644 --- a/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/GroupEntitiesSparkJob.java +++ b/dhp-workflows/dhp-dedup-openaire/src/main/java/eu/dnetlib/dhp/oa/dedup/GroupEntitiesSparkJob.java @@ -38,8 +38,7 @@ import scala.Tuple2; /** * Groups the graph content by entity identifier to ensure ID uniqueness */ -public class -GroupEntitiesSparkJob { +public class GroupEntitiesSparkJob { private static final Logger log = LoggerFactory.getLogger(GroupEntitiesSparkJob.class); diff --git a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala index 686a2f1f15..502cb370f8 100644 --- a/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala +++ b/dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/DoiBoostMappingUtil.scala @@ -245,6 +245,8 @@ object DoiBoostMappingUtil { if (item != null) { hb.setValue(item.officialname) hb.setKey(generateDSId(item.id)) + //TODO replace with the one above as soon as the new HBM will be used + //hb.setKey(item.id) if (item.openAccess) { i.setAccessright(getOpenAccessQualifier()) i.getAccessright.setOpenAccessRoute(OpenAccessRoute.gold) 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 deleted file mode 100644 index 561d2bbf45..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Aggregators.scala +++ /dev/null @@ -1,54 +0,0 @@ -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) {} -case class HostedByInfo(id: String, officialname: String, journal_id: String, provenance : String, id_type: String) {} - -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 deleted file mode 100644 index b07e33cd19..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/Constants.java +++ /dev/null @@ -1,15 +0,0 @@ -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 deleted file mode 100644 index d397886a32..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/GetCSV.java +++ /dev/null @@ -1,111 +0,0 @@ -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/model/DOAJModel.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/DOAJModel.java deleted file mode 100644 index fe1d14a763..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/DOAJModel.java +++ /dev/null @@ -1,53 +0,0 @@ -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 deleted file mode 100644 index 309f74eea5..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/model/UnibiGoldModel.java +++ /dev/null @@ -1,44 +0,0 @@ -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/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala new file mode 100644 index 0000000000..6a9346ed50 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala @@ -0,0 +1,97 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap + +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) {} +case class HostedByInfo(id: String, officialname: String, journal_id: String, provenance : String, id_type: String) {} + +object Aggregators { + + + + def getId(s1:String, s2:String) : String = { + if (s1.startsWith("10|")){ + return s1} + s2 + } + + def getValue(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 + + def explodeHostedByItemType(df: Dataset[(String, HostedByItemType)]): Dataset[(String, HostedByItemType)] = { + val transformedData : Dataset[(String, HostedByItemType)] = df + .groupByKey(_._1)(Encoders.STRING) + .agg(Aggregators.hostedByAggregator1) + .map{ + case (id:String , res:(String, HostedByItemType)) => res + }(Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType])) + + transformedData + } + + val hostedByAggregator1: TypedColumn[(String, HostedByItemType), (String, HostedByItemType)] = new Aggregator[(String, HostedByItemType), (String, HostedByItemType), (String, HostedByItemType)] { + override def zero: (String, HostedByItemType) = ("", HostedByItemType("","","","","",false)) + override def reduce(b: (String, HostedByItemType), a:(String,HostedByItemType)): (String, HostedByItemType) = { + return merge(b, a) + } + override def merge(b1: (String, HostedByItemType), b2: (String, HostedByItemType)): (String, HostedByItemType) = { + if (b1 == null){ + return b2 + } + if(b2 == null){ + return b1 + } + if(b1._2.id.startsWith("10|")){ + return (b1._1, HostedByItemType(b1._2.id, b1._2.officialname, b1._2.issn, b1._2.eissn, b1._2.lissn, b1._2.openAccess || b2._2.openAccess)) + + } + return (b2._1, HostedByItemType(b2._2.id, b2._2.officialname, b2._2.issn, b2._2.eissn, b2._2.lissn, b1._2.openAccess || b2._2.openAccess)) + + } + override def finish(reduction: (String,HostedByItemType)): (String, HostedByItemType) = reduction + override def bufferEncoder: Encoder[(String,HostedByItemType)] = Encoders.tuple(Encoders.STRING,Encoders.product[HostedByItemType]) + + override def outputEncoder: Encoder[(String,HostedByItemType)] = Encoders.tuple(Encoders.STRING,Encoders.product[HostedByItemType]) + }.toColumn + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Constants.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Constants.java new file mode 100644 index 0000000000..b29877a48f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Constants.java @@ -0,0 +1,13 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap; + +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/hostedbymap/GetCSV.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/GetCSV.java new file mode 100644 index 0000000000..9516cf6f76 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/GetCSV.java @@ -0,0 +1,107 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap; + +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.nio.charset.Charset; +import java.nio.charset.StandardCharsets; +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.FSDataOutputStream; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; + +import com.fasterxml.jackson.databind.ObjectMapper; +import com.opencsv.bean.CsvToBeanBuilder; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; + +public class GetCSV { + private static final Log log = LogFactory.getLog(eu.dnetlib.dhp.oa.graph.hostedbymap.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("workingPath"); + 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/hostedbymap/SparkProduceHostedByMap.scala similarity index 76% rename from dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostebymap/SparkPrepareHostedByMapData.scala rename to dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala index b66e972818..c44f2cbed7 100644 --- 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/hostedbymap/SparkProduceHostedByMap.scala @@ -1,17 +1,23 @@ -package eu.dnetlib.dhp.oa.graph.hostebymap +package eu.dnetlib.dhp.oa.graph.hostedbymap import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.oa.graph.hostebymap.model.{DOAJModel, UnibiGoldModel} -import eu.dnetlib.dhp.schema.oaf.{Datasource} +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DOAJModel, UnibiGoldModel} +import eu.dnetlib.dhp.schema.oaf.Datasource 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 com.fasterxml.jackson.databind.ObjectMapper +import org.apache.hadoop.conf.Configuration +import org.apache.hadoop.fs.FileSystem +import org.apache.hadoop.fs.Path +import java.io.PrintWriter -object SparkPrepareHostedByMapData { +import org.apache.hadoop.io.compress.GzipCodec + + +object SparkProduceHostedByMap { implicit val tupleForJoinEncoder: Encoder[(String, HostedByItemType)] = Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType]) @@ -37,24 +43,32 @@ object SparkPrepareHostedByMapData { } } -// 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 toHostedByMap(input: (String, HostedByItemType)): String = { + import org.json4s.jackson.Serialization + + implicit val formats = org.json4s.DefaultFormats + + val map: Map [String, HostedByItemType] = Map (input._1 -> input._2 ) + + Serialization.write(map) + + + } + + /** + * + def toHostedByMap(input: Map[String, HostedByItemType]): String = { + import org.json4s.jackson.Serialization + + implicit val formats = org.json4s.DefaultFormats + + + + Serialization.write(input) + + + } + */ def getHostedByItemType(id:String, officialname: String, issn:String, eissn:String, issnl:String, oa:Boolean): HostedByItemType = { if(issn != null){ @@ -166,11 +180,31 @@ object SparkPrepareHostedByMapData { } + + def writeToHDFS(input: Array[String], outputPath: String, hdfsNameNode : String):Unit = { + val conf = new Configuration() + + conf.set("fs.defaultFS", hdfsNameNode) + val fs= FileSystem.get(conf) + val output = fs.create(new Path(outputPath)) + val writer = new PrintWriter(output) + try { + input.foreach(hbi => writer.println(hbi)) + } + finally { + writer.close() + + } + + } + + + 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"))) + val parser = new ArgumentApplicationParser(IOUtils.toString(getClass.getResourceAsStream("/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_params.json"))) parser.parseArgument(args) val spark: SparkSession = SparkSession @@ -179,11 +213,10 @@ object SparkPrepareHostedByMapData { .appName(getClass.getSimpleName) .master(parser.get("master")).getOrCreate() - import spark.implicits._ val datasourcePath = parser.get("datasourcePath") val workingDirPath = parser.get("workingPath") - + val outputPath = parser.get("outputPath") implicit val formats = DefaultFormats @@ -191,29 +224,15 @@ object SparkPrepareHostedByMapData { logger.info("Getting the Datasources") - // val doajDataset: Dataset[DOAJModel] = spark.read.textFile(workingDirPath + "/doaj").as[DOAJModel] - val dats : Dataset[HostedByItemType] = - oaHostedByDataset(spark, datasourcePath) + Aggregators.explodeHostedByItemType(oaHostedByDataset(spark, datasourcePath) .union(goldHostedByDataset(spark, workingDirPath + "/unibi_gold")) .union(doajHostedByDataset(spark, workingDirPath + "/doaj")) - dats.flatMap(hbi => toList(hbi)) - .groupByKey(_._1) + .flatMap(hbi => toList(hbi))).filter(hbi => hbi._2.id.startsWith("10|")) + .map(hbi => toHostedByMap(hbi))(Encoders.STRING) + .rdd.saveAsTextFile(outputPath + "/hostedByMap", classOf[GzipCodec]) -// -// - -// - -// -// Aggregators.createHostedByItemTypes(oa.joinWith(doaj, oa.col("journal_id").equalTo(doaj.col("journal_id")), "left") -// .joinWith(gold, $"_1.col('journal_id')".equalTo(gold.col("journal_id")), "left").map(toHostedByItemType) -// .filter(i => i != null)) -// .flatMap(toHostedByMap) -// .write.mode(SaveMode.Overwrite).save(s"$workingDirPath/HostedByMap") -// -// } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java new file mode 100644 index 0000000000..ba804b939d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DOAJModel.java @@ -0,0 +1,52 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.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/hostedbymap/model/UnibiGoldModel.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/UnibiGoldModel.java new file mode 100644 index 0000000000..0927a136be --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/UnibiGoldModel.java @@ -0,0 +1,45 @@ + +package eu.dnetlib.dhp.oa.graph.hostedbymap.model; + +import java.io.Serializable; + +import com.opencsv.bean.CsvBindByName; + +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/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_csv_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_csv_parameters.json new file mode 100644 index 0000000000..fba048343b --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/download_csv_parameters.json @@ -0,0 +1,37 @@ + +[ + + { + "paramName":"fu", + "paramLongName":"fileURL", + "paramDescription": "the url to download the csv file ", + "paramRequired": true + }, + + { + "paramName":"wp", + "paramLongName":"workingPath", + "paramDescription": "the path where to find the pre-processed data for unibi gold list and doj artciles", + "paramRequired": true + }, + { + "paramName": "hnn", + "paramLongName": "hdfsNameNode", + "paramDescription": "the path used to store the HostedByMap", + "paramRequired": true + }, + { + "paramName": "cfn", + "paramLongName": "classForName", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": true + }, + { + "paramName": "sr", + "paramLongName": "replace", + "paramDescription": "true if the input file has to be cleaned before parsing", + "paramRequired": false + } +] + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_params.json new file mode 100644 index 0000000000..9173b78aed --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_params.json @@ -0,0 +1,38 @@ + +[ + + { + "paramName":"dsp", + "paramLongName":"datasourcePath", + "paramDescription": "the path to the datasource ", + "paramRequired": true + }, + + { + "paramName":"wp", + "paramLongName":"workingPath", + "paramDescription": "the path where to find the pre-processed data for unibi gold list and doj artciles", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "the path used to store the HostedByMap", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": true + } +] + + + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/config-default.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/config-default.xml new file mode 100644 index 0000000000..e5ec3d0aee --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/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/hostedbymap/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml new file mode 100644 index 0000000000..ecf6c3b316 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml @@ -0,0 +1,148 @@ + + + + + sourcePath + the source path + + + outputPath + the output path + + + 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())}] + + + + + + + + + + + + + + + + + + + + + eu.dnetlib.dhp.oa.graph.hostedbymap.GetCSV + --hdfsNameNode${nameNode} + --fileURL${unibiFileURL} + --workingPath${workingDir}/unibi_gold + --classForNameeu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel + + + + + + + + eu.dnetlib.dhp.oa.graph.hostedbymap.GetCSV + --hdfsNameNode${nameNode} + --fileURL${doajFileURL} + --workingPath${workingDir}/doaj + --classForNameeu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel + --replacetrue + + + + + + + + + + + + yarn-cluster + Produce the new HostedByMap + eu.dnetlib.dhp.oa.graph.hostedbymap.SparkProduceHostedByMap + 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} + + --datasourcePath${sourcePath}/datasource + --workingPath${workingDir} + --outputPath${outputPath} + --masteryarn-cluster + + + + + + + + + + \ No newline at end of file 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 index 8e5657bfc1..2ed76a72ac 100644 --- 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 @@ -1,19 +1,14 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap -import java.sql.Timestamp - -import com.fasterxml.jackson.databind.ObjectMapper -import eu.dnetlib.dhp.oa.graph.hostebymap.{Constants, HostedByInfo, SparkPrepareHostedByMapData} +import eu.dnetlib.dhp.oa.graph.hostedbymap.{Aggregators, Constants, HostedByInfo, HostedByItemType, SparkProduceHostedByMap} import eu.dnetlib.dhp.schema.oaf.Datasource import org.apache.spark.SparkConf import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} 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.collection.mutable.ListBuffer -import scala.io.Source +import org.junit.jupiter.api.Assertions._ +import org.json4s.jackson.Serialization.write class TestPreprocess extends java.io.Serializable{ @@ -21,19 +16,14 @@ class TestPreprocess extends java.io.Serializable{ implicit val schema = Encoders.product[HostedByInfo] + def toHBIString (hbi:HostedByItemType): String = { + implicit val formats = DefaultFormats + + write(hbi) + } @Test def readDatasource():Unit = { - - - import org.apache.spark.sql.Encoders - implicit val formats = DefaultFormats - - val logger: Logger = LoggerFactory.getLogger(getClass) - val mapper = new ObjectMapper() - - - val conf = new SparkConf() conf.setMaster("local[*]") conf.set("spark.driver.host", "localhost") @@ -45,25 +35,29 @@ class TestPreprocess extends java.io.Serializable{ .getOrCreate() val path = getClass.getResource("datasource.json").getPath + val ds :Dataset[HostedByItemType]= SparkProduceHostedByMap.oaHostedByDataset(spark, path) - println(SparkPrepareHostedByMapData.oaHostedByDataset(spark, path).count) + assertEquals(9, ds.count) + assertEquals(8, ds.filter(hbi => !hbi.issn.equals("")).count) + assertEquals(5, ds.filter(hbi => !hbi.eissn.equals("")).count) + assertEquals(0, ds.filter(hbi => !hbi.lissn.equals("")).count) + assertEquals(0, ds.filter(hbi => hbi.issn.equals("") && hbi.eissn.equals("") && hbi.lissn.equals("")).count) + assertTrue(ds.filter(hbi => hbi.issn.equals("0212-8365")).count == 1) + assertTrue(ds.filter(hbi => hbi.eissn.equals("2253-900X")).count == 1) + assertTrue(ds.filter(hbi => hbi.issn.equals("0212-8365") && hbi.eissn.equals("2253-900X")).count == 1) + assertTrue(ds.filter(hbi => hbi.issn.equals("0212-8365") && hbi.officialname.equals("Thémata")).count == 1) + assertTrue(ds.filter(hbi => hbi.issn.equals("0212-8365") && hbi.id.equals("10|doajarticles::abbc9265bea9ff62776a1c39785af00c")).count == 1) + ds.foreach(hbi => assertTrue(hbi.id.startsWith("10|"))) + ds.foreach(hbi => println(toHBIString(hbi))) spark.close() } @Test def readGold():Unit = { - - implicit val formats = DefaultFormats - - val logger: Logger = LoggerFactory.getLogger(getClass) - val mapper = new ObjectMapper() - - - val conf = new SparkConf() conf.setMaster("local[*]") conf.set("spark.driver.host", "localhost") @@ -76,23 +70,27 @@ class TestPreprocess extends java.io.Serializable{ val path = getClass.getResource("unibi_transformed.json").getPath - println(SparkPrepareHostedByMapData.goldHostedByDataset(spark, path).count) + val ds :Dataset[HostedByItemType]= SparkProduceHostedByMap.goldHostedByDataset(spark, path) + assertEquals(29, ds.count) + assertEquals(29, ds.filter(hbi => !hbi.issn.equals("")).count) + assertEquals(0, ds.filter(hbi => !hbi.eissn.equals("")).count) + assertEquals(29, ds.filter(hbi => !hbi.lissn.equals("")).count) + + assertEquals(0, ds.filter(hbi => hbi.issn.equals("") && hbi.eissn.equals("") && hbi.lissn.equals("")).count) + + assertTrue(ds.filter(hbi => hbi.issn.equals("2239-6101")).first().officialname.equals("European journal of sustainable development.")) + assertTrue(ds.filter(hbi => hbi.issn.equals("2239-6101")).first().lissn.equals("2239-5938")) + assertTrue(ds.filter(hbi => hbi.issn.equals("2239-6101")).count == 1) + ds.foreach(hbi => assertTrue(hbi.id.equals(Constants.UNIBI))) + ds.foreach(hbi => println(toHBIString(hbi))) spark.close() } @Test def readDoaj():Unit = { - - implicit val formats = DefaultFormats - - val logger: Logger = LoggerFactory.getLogger(getClass) - val mapper = new ObjectMapper() - - - val conf = new SparkConf() conf.setMaster("local[*]") conf.set("spark.driver.host", "localhost") @@ -104,14 +102,69 @@ class TestPreprocess extends java.io.Serializable{ .getOrCreate() val path = getClass.getResource("doaj_transformed.json").getPath + val ds :Dataset[HostedByItemType]= SparkProduceHostedByMap.doajHostedByDataset(spark, path) - println(SparkPrepareHostedByMapData.doajHostedByDataset(spark, path).count) + assertEquals(25, ds.count) + assertEquals(14, ds.filter(hbi => !hbi.issn.equals("")).count) + assertEquals(21, ds.filter(hbi => !hbi.eissn.equals("")).count) + assertEquals(0, ds.filter(hbi => !hbi.lissn.equals("")).count) + assertEquals(0, ds.filter(hbi => hbi.issn.equals("") && hbi.eissn.equals("") && hbi.lissn.equals("")).count) + + assertTrue(ds.filter(hbi => hbi.issn.equals("2077-3099")).first().officialname.equals("Journal of Space Technology")) + assertTrue(ds.filter(hbi => hbi.issn.equals("2077-3099")).first().eissn.equals("2411-5029")) + assertTrue(ds.filter(hbi => hbi.issn.equals("2077-3099")).count == 1) + assertTrue(ds.filter(hbi => hbi.eissn.equals("2077-2955")).first().issn.equals("")) + ds.foreach(hbi => assertTrue(hbi.id.equals(Constants.DOAJ))) + ds.foreach(hbi => println(toHBIString(hbi))) spark.close() } + @Test + def testAggregator() : Unit = { + + 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 tmp = SparkProduceHostedByMap.oaHostedByDataset(spark, getClass.getResource("datasource.json").getPath) + .union(SparkProduceHostedByMap.goldHostedByDataset(spark,getClass.getResource("unibi_transformed.json").getPath)) + .union(SparkProduceHostedByMap.doajHostedByDataset(spark, getClass.getResource("doaj_transformed.json").getPath)) + .flatMap(hbi => SparkProduceHostedByMap.toList(hbi))(Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType])) + + assertEquals(106, tmp.count) + assertEquals(82, tmp.map(i => i._1)(Encoders.STRING).distinct().count) + + + val ds :Dataset[(String, HostedByItemType)] = Aggregators.explodeHostedByItemType(SparkProduceHostedByMap.oaHostedByDataset(spark, getClass.getResource("datasource.json").getPath) + .union(SparkProduceHostedByMap.goldHostedByDataset(spark,getClass.getResource("unibi_transformed.json").getPath)) + .union(SparkProduceHostedByMap.doajHostedByDataset(spark, getClass.getResource("doaj_transformed.json").getPath)) + .flatMap(hbi => SparkProduceHostedByMap.toList(hbi))(Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType]))) + + assertEquals(82, ds.count) + + assertEquals(13, ds.filter(i => i._2.id.startsWith("10|")).count) + + assertTrue(ds.filter(i => i._1.equals("2077-3757")).first()._2.id.startsWith("10|")) + assertTrue(ds.filter(i => i._1.equals("2077-3757")).first()._2.openAccess) + assertEquals(1, ds.filter(i => i._1.equals("2077-3757")).count) + + val hbmap : Dataset[String] = ds.filter(hbi => hbi._2.id.startsWith("10|")).map(SparkProduceHostedByMap.toHostedByMap)(Encoders.STRING) + + hbmap.foreach(entry => println(entry)) + 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 index 01c70502c7..f886b275b4 100644 --- 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 @@ -1,111 +1,109 @@ + package eu.dnetlib.dhp.oa.graph.hostedbymap; +import java.io.*; +import java.net.URL; +import java.net.URLConnection; +import java.nio.charset.Charset; +import java.util.List; + +import org.junit.jupiter.api.Test; + 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; +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel; -public class TestReadCSV { +public class TestReadCSV { - @Test - public void testCSVUnibi() throws FileNotFoundException { + @Test + public void testCSVUnibi() throws FileNotFoundException { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/hostedbymap/unibiGold.csv") + .getPath(); - 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(); - List beans = new CsvToBeanBuilder(new FileReader(sourcePath)) - .withType(UnibiGoldModel.class) - .build() - .parse(); + ObjectMapper mapper = new ObjectMapper(); - ObjectMapper mapper = new ObjectMapper(); + beans.forEach(r -> { + try { + System.out.println(mapper.writeValueAsString(r)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + }); - 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"); - @Test - public void testCSVUrlUnibi() throws IOException { + BufferedReader in = new BufferedReader(new InputStreamReader(csv.openStream())); + ObjectMapper mapper = new ObjectMapper(); - URL csv = new URL("https://pub.uni-bielefeld.de/download/2944717/2944718/issn_gold_oa_version_4.csv"); + new CsvToBeanBuilder(in) + .withType(eu.dnetlib.dhp.oa.graph.hostedbymap.model.UnibiGoldModel.class) + .build() + .parse() + .forEach(line -> - BufferedReader in = new BufferedReader(new InputStreamReader(csv.openStream())); - ObjectMapper mapper = new ObjectMapper(); + { + try { + System.out.println(mapper.writeValueAsString(line)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + } - 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(); - @Test - public void testCSVUrlDOAJ() throws IOException { + new CsvToBeanBuilder(in) + .withType(eu.dnetlib.dhp.oa.graph.hostedbymap.model.DOAJModel.class) + .withMultilineLimit(1) + .build() + .parse() + .forEach(lline -> - 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(); + { + try { + System.out.println(mapper.writeValueAsString(lline)); + } catch (JsonProcessingException e) { + e.printStackTrace(); + } + } - 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/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java index c41a6c68c0..63f18a803a 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MappersTest.java @@ -1,13 +1,13 @@ package eu.dnetlib.dhp.oa.graph.raw; -import com.fasterxml.jackson.databind.ObjectMapper; -import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; -import eu.dnetlib.dhp.schema.common.ModelConstants; -import eu.dnetlib.dhp.schema.oaf.*; -import eu.dnetlib.dhp.schema.oaf.utils.PidType; -import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; +import static org.junit.jupiter.api.Assertions.*; +import static org.mockito.Mockito.lenient; + +import java.io.IOException; +import java.util.List; +import java.util.Optional; + import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; import org.junit.jupiter.api.BeforeEach; @@ -16,12 +16,14 @@ import org.junit.jupiter.api.extension.ExtendWith; import org.mockito.Mock; import org.mockito.junit.jupiter.MockitoExtension; -import java.io.IOException; -import java.util.List; -import java.util.Optional; +import com.fasterxml.jackson.databind.ObjectMapper; -import static org.junit.jupiter.api.Assertions.*; -import static org.mockito.Mockito.lenient; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.oa.graph.clean.GraphCleaningFunctionsTest; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.PidType; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; @ExtendWith(MockitoExtension.class) public class MappersTest { @@ -340,7 +342,7 @@ public class MappersTest { assertEquals(2, p.getOriginalId().size()); assertTrue(p.getOriginalId().stream().anyMatch(oid -> oid.equals("oai:pub.uni-bielefeld.de:2949739"))); - //assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); + // assertEquals("oai:pub.uni-bielefeld.de:2949739", p.getOriginalId().get(0)); assertValidId(p.getCollectedfrom().get(0).getKey()); assertTrue(p.getAuthor().size() > 0); 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 index 818aaa7167..4467c702f6 100644 --- 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 @@ -1,6 +1,6 @@ {"accessinfopackage":[],"collectedfrom":[{"key":"10|driver______::bee53aa31dc2cbb538c10c2b65fa5824","value":"DOAJ-Articles"}],"dataInfo":null,"dataprovider":{"dataInfo":null,"value":false},"datasourcetype":{"classid":"pubsrepository::journal","classname":"Journal","schemeid":"dnet:datasource_typologies","schemename":"dnet:datasource_typologies"},"dateofcollection":"2020-03-01","englishname":{"dataInfo":null,"value":"Известия высших учебных заведений: Проблемы энергетики"},"extraInfo":[],"id":"10|doajarticles::0ab37b7620eb9a73ac95d3ca4320c97d","journal":{"dataInfo":null,"issnPrinted":"1998-9903","name":"Известия высших учебных заведений: Проблемы энергетики"},"lastupdatetimestamp":1626336932282,"latitude":{"dataInfo":null,"value":"0.0"},"longitude":{"dataInfo":null,"value":"0.0"},"namespaceprefix":{"dataInfo":null,"value":"doaj19989903"},"odcontenttypes":[{"dataInfo":null,"value":"Journal articles"}],"odlanguages":[],"odnumberofitems":{"dataInfo":null,"value":"0.0"},"officialname":{"dataInfo":null,"value":"Известия высших учебных заведений: Проблемы энергетики"},"openairecompatibility":{"classid":"hostedBy","classname":"collected from a compatible aggregator","schemeid":"dnet:datasourceCompatibilityLevel","schemename":"dnet:datasourceCompatibilityLevel"},"originalId":["doajarticles::1998-9903"],"pid":[],"policies":[],"serviceprovider":{"dataInfo":null,"value":false},"subjects":[{"dataInfo":null,"qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:subject_classification_typologies","schemename":"dnet:subject_classification_typologies"},"value":"Technology: Electrical engineering. Electronics. Nuclear engineering: Production of electric energy or power. Powerplants. 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a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doajHostedByItem b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doajHostedByItem new file mode 100644 index 0000000000..effd0dd601 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/doajHostedByItem @@ -0,0 +1,25 @@ +{"id":"doaj","officialname":"Lëd i Sneg","issn":"2076-6734","eissn":"2412-3765","lissn":"","openAccess":true} +{"id":"doaj","officialname":"Компьютерные исследования и моделирование","issn":"2076-7633","eissn":"2077-6853","lissn":"","openAccess":true} +{"id":"doaj","officialname":" Историко-биологические исследования","issn":"2076-8176","eissn":"2500-1221","lissn":"","openAccess":true} +{"id":"doaj","officialname":"Інформаційні технології і засоби навчання","issn":"2076-8184","eissn":"","lissn":"","openAccess":true} +{"id":"doaj","officialname":"Revue Internationale de Pédagogie de 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+{"id":"doaj","officialname":"Edumecentro","issn":"","eissn":"2077-2874","lissn":"","openAccess":true} +{"id":"doaj","officialname":"Monteverdia","issn":"","eissn":"2077-2890","lissn":"","openAccess":true} +{"id":"doaj","officialname":"Transformación","issn":"","eissn":"2077-2955","lissn":"","openAccess":true} +{"id":"doaj","officialname":"Journal of Space Technology","issn":"2077-3099","eissn":"2411-5029","lissn":"","openAccess":true} +{"id":"doaj","officialname":"Revue de Primatologie","issn":"","eissn":"2077-3757","lissn":"","openAccess":true} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibyHostedByItem b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibyHostedByItem new file mode 100644 index 0000000000..403ffdf5dc --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/unibyHostedByItem @@ -0,0 +1,29 @@ +{"id":"unibi","officialname":"JIMKESMAS (Jurnal Ilmiah Mahasiswa Kesehatan Masyarakat)","issn":"2502-731X","eissn":"","lissn":"2502-731X","openAccess":true} +{"id":"unibi","officialname":"Jurnal ilmu informasi, perpustakaan, dan kearsipan","issn":"2502-7409","eissn":"","lissn":"1411-0253","openAccess":true} +{"id":"unibi","officialname":"At-Tadbir : jurnal ilmiah manajemen","issn":"2502-7433","eissn":"","lissn":"2502-7433","openAccess":true} +{"id":"unibi","officialname":"Jurnal Kesehatan Panrita Husada.","issn":"2502-745X","eissn":"","lissn":"2502-745X","openAccess":true} +{"id":"unibi","officialname":"ELang journal (An English Education journal)","issn":"2502-7549","eissn":"","lissn":"2502-7549","openAccess":true} +{"id":"unibi","officialname":"̒Ulūm-i darmāngāhī-i dāmpizishkī-i Īrān.","issn":"2423-3633","eissn":"","lissn":"2423-3625","openAccess":true} +{"id":"unibi","officialname":"Pizhūhishnāmah-i ̒ilm/sanjī.","issn":"2423-5563","eissn":"","lissn":"2423-3773","openAccess":true} +{"id":"unibi","officialname":"Iranian journal of animal biosystematics.","issn":"1735-434X","eissn":"","lissn":"1735-434X","openAccess":true} +{"id":"unibi","officialname":"Majallah-i jangal-i Īrān.","issn":"2423-4435","eissn":"","lissn":"2008-6113","openAccess":true} +{"id":"unibi","officialname":"Ābziyān-i zinatī.","issn":"2423-4575","eissn":"","lissn":"2423-4575","openAccess":true} +{"id":"unibi","officialname":"Pizhūhishnāmah-i ravābiṭ-i biyn/al- milal.","issn":"2423-4974","eissn":"","lissn":"2423-4974","openAccess":true} +{"id":"unibi","officialname":"AIHM journal club.","issn":"2380-0607","eissn":"","lissn":"2380-0607","openAccess":true} +{"id":"unibi","officialname":"Frontiers.","issn":"1085-4568","eissn":"","lissn":"1085-4568","openAccess":true} +{"id":"unibi","officialname":"˜The œjournal of contemporary archival studies.","issn":"2380-8845","eissn":"","lissn":"2380-8845","openAccess":true} +{"id":"unibi","officialname":"International journal of complementary & alternative medicine.","issn":"2381-1803","eissn":"","lissn":"2381-1803","openAccess":true} +{"id":"unibi","officialname":"Palapala.","issn":"2381-2478","eissn":"","lissn":"2381-2478","openAccess":true} +{"id":"unibi","officialname":"Asia pacific journal of environment ecology and sustainable development.","issn":"2382-5170","eissn":"","lissn":"2382-5170","openAccess":true} +{"id":"unibi","officialname":"Majallah-i salāmat va bihdāsht","issn":"2382-9737","eissn":"","lissn":"2382-9737","openAccess":true} +{"id":"unibi","officialname":"UCT journal of research in science ,engineering and technology","issn":"2382-977X","eissn":"","lissn":"2382-977X","openAccess":true} +{"id":"unibi","officialname":"Bih/nizhādī-i giyāhān-i zirā̒ī va bāghī.","issn":"2382-9974","eissn":"","lissn":"2382-9974","openAccess":true} +{"id":"unibi","officialname":"Problemi endokrinnoï patologìï.","issn":"2227-4782","eissn":"","lissn":"2227-4782","openAccess":true} +{"id":"unibi","officialname":"Jurnal Kebijakan Pembangunan Daerah : Jurnal Penelitian dan Pengembangan Kebijakan Pembangunan Daerah.","issn":"2685-0079","eissn":"","lissn":"2597-4971","openAccess":true} +{"id":"unibi","officialname":"Hypermedia magazine.","issn":"2574-0075","eissn":"","lissn":"2574-0075","openAccess":true} +{"id":"unibi","officialname":"˜The œmuseum review.","issn":"2574-0296","eissn":"","lissn":"2574-0296","openAccess":true} +{"id":"unibi","officialname":"Bioactive compounds in health and disease.","issn":"2574-0334","eissn":"","lissn":"2574-0334","openAccess":true} +{"id":"unibi","officialname":"Journal of computer science integration.","issn":"2574-108X","eissn":"","lissn":"2574-108X","openAccess":true} +{"id":"unibi","officialname":"Child and adolescent obesity.","issn":"2574-254X","eissn":"","lissn":"2574-254X","openAccess":true} +{"id":"unibi","officialname":"Journal of research on the college president.","issn":"2574-3325","eissn":"","lissn":"2574-3325","openAccess":true} +{"id":"unibi","officialname":"European journal of sustainable development.","issn":"2239-6101","eissn":"","lissn":"2239-5938","openAccess":true} \ No newline at end of file From 613bd3bde0076113dd37a64d2efbc23ec8e9ec61 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 30 Jul 2021 17:54:45 +0200 Subject: [PATCH 06/51] Hosted By Map - refactor of the first attemp to prepare a new hosted by map dependent on the datasource in the graph and on two external sources: the gold list from unibi ad the doaj list of open access journal. Both the lists are downloaded from provided url parameter --- .../graph/hostedbymap/SparkProduceHostedByMap.scala | 13 ------------- 1 file changed, 13 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala index c44f2cbed7..ca5e82a4a1 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala @@ -55,20 +55,7 @@ object SparkProduceHostedByMap { } - /** - * - def toHostedByMap(input: Map[String, HostedByItemType]): String = { - import org.json4s.jackson.Serialization - implicit val formats = org.json4s.DefaultFormats - - - - Serialization.write(input) - - - } - */ def getHostedByItemType(id:String, officialname: String, issn:String, eissn:String, issnl:String, oa:Boolean): HostedByItemType = { if(issn != null){ From d8b9b0553b7c89b7831625dd3804384c9dab4e03 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 30 Jul 2021 17:55:39 +0200 Subject: [PATCH 07/51] Hosted By Map - model classes to store the intermediate information to be used to apply the hosted by map --- .../hostedbymap/model/DatasourceInfo.java | 72 +++++++++++++++++++ .../graph/hostedbymap/model/EntityInfo.java | 69 ++++++++++++++++++ 2 files changed, 141 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DatasourceInfo.java create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/EntityInfo.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DatasourceInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DatasourceInfo.java new file mode 100644 index 0000000000..f5ac8f70c5 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DatasourceInfo.java @@ -0,0 +1,72 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap.model; + +import java.io.Serializable; + +public class DatasourceInfo implements Serializable { + private String id; + private String officialname; + private String issn; + private String eissn; + private String lissn; + private Boolean openAccess; + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getOfficialname() { + return officialname; + } + + public void setOfficialname(String officialname) { + this.officialname = officialname; + } + + 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 getLissn() { + return lissn; + } + + public void setLissn(String lissn) { + this.lissn = lissn; + } + + public Boolean getOpenAccess() { + return openAccess; + } + + public void setOpenAccess(Boolean openAccess) { + this.openAccess = openAccess; + } + + public static DatasourceInfo newInstance(String id, String officialname, String issn, String eissn, String lissn){ + DatasourceInfo di = new DatasourceInfo(); + di.id = id; + di.officialname = officialname; + di.issn = (issn != null) ? issn : "" ; + di.eissn = (eissn != null) ? eissn:""; + di.lissn = (lissn != null) ? lissn : ""; + di.openAccess = false; + + return di; + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/EntityInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/EntityInfo.java new file mode 100644 index 0000000000..7bf9d05982 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/EntityInfo.java @@ -0,0 +1,69 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap.model; + +import java.io.Serializable; + +public class EntityInfo implements Serializable { + private String id; + private String journal_id; + private String name; + private Boolean openaccess; + private String hb_id; + + + + public String getId() { + return id; + } + + public void setId(String id) { + this.id = id; + } + + public String getJournal_id() { + return journal_id; + } + + public void setJournal_id(String journal_id) { + this.journal_id = journal_id; + } + + public String getName() { + return name; + } + + public void setName(String name) { + this.name = name; + } + + public Boolean getOpenaccess() { + return openaccess; + } + + public void setOpenaccess(Boolean openaccess) { + this.openaccess = openaccess; + } + + public String getHb_id() { + return hb_id; + } + + public void setHb_id(String hb_id) { + this.hb_id = hb_id; + } + + public static EntityInfo newInstance(String id, String j_id, String name){ + return newInstance(id, j_id, name, false); + + } + + public static EntityInfo newInstance(String id, String j_id, String name, Boolean openaccess){ + EntityInfo pi = new EntityInfo(); + pi.id = id; + pi.journal_id = j_id; + pi.name = name; + pi.openaccess = openaccess; + pi.hb_id = ""; + return pi; + + } +} From 7c6ea2f4c700c3ce59dd78e5e4eed4ea8c198c5e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 30 Jul 2021 17:56:27 +0200 Subject: [PATCH 08/51] Hosted By Map - first attempt for the creation of intermedia information to be used to applu the hosted by map on the graph entities --- .../oa/graph/hostedbymap/Aggregators.scala | 113 +++++++++----- .../SparkPrepareHostedByInfoToApply.scala | 147 ++++++++++++++++++ 2 files changed, 225 insertions(+), 35 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala index 6a9346ed50..8077efe302 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala @@ -1,5 +1,6 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo import org.apache.spark.sql.{Dataset, Encoder, Encoders, TypedColumn} import org.apache.spark.sql.expressions.Aggregator @@ -25,43 +26,10 @@ object Aggregators { } - 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 - def explodeHostedByItemType(df: Dataset[(String, HostedByItemType)]): Dataset[(String, HostedByItemType)] = { val transformedData : Dataset[(String, HostedByItemType)] = df .groupByKey(_._1)(Encoders.STRING) - .agg(Aggregators.hostedByAggregator1) + .agg(Aggregators.hostedByAggregator) .map{ case (id:String , res:(String, HostedByItemType)) => res }(Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType])) @@ -69,7 +37,7 @@ object Aggregators { transformedData } - val hostedByAggregator1: TypedColumn[(String, HostedByItemType), (String, HostedByItemType)] = new Aggregator[(String, HostedByItemType), (String, HostedByItemType), (String, HostedByItemType)] { + val hostedByAggregator: TypedColumn[(String, HostedByItemType), (String, HostedByItemType)] = new Aggregator[(String, HostedByItemType), (String, HostedByItemType), (String, HostedByItemType)] { override def zero: (String, HostedByItemType) = ("", HostedByItemType("","","","","",false)) override def reduce(b: (String, HostedByItemType), a:(String,HostedByItemType)): (String, HostedByItemType) = { return merge(b, a) @@ -94,4 +62,79 @@ object Aggregators { override def outputEncoder: Encoder[(String,HostedByItemType)] = Encoders.tuple(Encoders.STRING,Encoders.product[HostedByItemType]) }.toColumn + def hostedByToSingleDSId(df: Dataset[ HostedByItemType]): Dataset[ HostedByItemType] = { + val transformedData : Dataset[HostedByItemType] = df + .groupByKey(_.id)(Encoders.STRING) + .agg(Aggregators.hostedByToDSAggregator) + .map{ + case (id:String , res: HostedByItemType) => res + }(Encoders.product[HostedByItemType]) + + transformedData + } + + def hostedByToDSAggregator: 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 + } + if(!b1.id.equals("")){ + return HostedByItemType(b1.id, b1.officialname, b1.issn, b1.eissn, b1.lissn, b1.openAccess || b2.openAccess) + + } + return HostedByItemType(b2.id, b2.officialname, b2.issn, b2.eissn, 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 + + + def resultToSingleIdAggregator: TypedColumn[EntityInfo, EntityInfo] = new Aggregator[EntityInfo, EntityInfo, EntityInfo]{ + override def zero: EntityInfo = EntityInfo.newInstance("","","") + + override def reduce(b: EntityInfo, a:EntityInfo): EntityInfo = { + return merge(b, a) + } + override def merge(b1: EntityInfo, b2: EntityInfo): EntityInfo = { + if (b1 == null){ + return b2 + } + if(b2 == null){ + return b1 + } + if(!b1.getHb_id.equals("")){ + b1.setOpenaccess(b1.getOpenaccess || b2.getOpenaccess) + } + b2.setOpenaccess(b1.getOpenaccess || b2.getOpenaccess) + b2 + + } + override def finish(reduction: EntityInfo): EntityInfo = reduction + override def bufferEncoder: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + + override def outputEncoder: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + }.toColumn + + def resultToSingleId(df:Dataset[EntityInfo]): Dataset[EntityInfo] = { + val transformedData : Dataset[EntityInfo] = df + .groupByKey(_.getId)(Encoders.STRING) + .agg(Aggregators.resultToSingleIdAggregator) + .map{ + case (id:String , res: EntityInfo) => res + }(Encoders.bean(classOf[EntityInfo])) + + transformedData + } + } diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala new file mode 100644 index 0000000000..03ab09d8e8 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala @@ -0,0 +1,147 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DatasourceInfo, EntityInfo} +import eu.dnetlib.dhp.schema.oaf.{Datasource, Journal, Publication} +import org.apache.commons.io.IOUtils +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} +import org.json4s +import org.json4s.DefaultFormats +import org.json4s.jackson.JsonMethods.parse +import org.slf4j.{Logger, LoggerFactory} + +object SparkPrepareHostedByInfoToApply { + + + implicit val mapEncoderDSInfo: Encoder[DatasourceInfo] = Encoders.kryo[DatasourceInfo] + implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.kryo[EntityInfo] + + def getList(id: String, j: Journal, name: String ) : List[EntityInfo] = { + var lst:List[EntityInfo] = List() + + + if (j.getIssnLinking != null && !j.getIssnLinking.equals("")){ + lst = EntityInfo.newInstance(id, j.getIssnLinking, name) :: lst + } + if (j.getIssnOnline != null && !j.getIssnOnline.equals("")){ + lst = EntityInfo.newInstance(id, j.getIssnOnline, name) :: lst + } + if (j.getIssnPrinted != null && !j.getIssnPrinted.equals("")){ + lst = EntityInfo.newInstance(id, j.getIssnPrinted, name) :: lst + } + lst + } + + def prepareResultInfo(spark:SparkSession, publicationPath:String) : Dataset[EntityInfo] = { + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication]) + + val mapper = new ObjectMapper() + + val dd : Dataset[Publication] = spark.read.textFile(publicationPath) + .map(r => mapper.readValue(r, classOf[Publication])) + + dd.filter(p => p.getJournal != null ).flatMap(p => getList(p.getId, p.getJournal, "")) + + } + + + + def prepareDatasourceInfo(spark:SparkSession, datasourcePath:String) : Dataset[DatasourceInfo] = { + implicit val mapEncoderDats: Encoder[Datasource] = Encoders.bean(classOf[Datasource]) + + val mapper = new ObjectMapper() + + val dd : Dataset[Datasource] = spark.read.textFile(datasourcePath) + .map(r => mapper.readValue(r, classOf[Datasource])) + + dd.filter(d => d.getJournal != null ).map(d => DatasourceInfo.newInstance(d.getId, d.getOfficialname.getValue, + d.getJournal.getIssnPrinted, d.getJournal.getIssnOnline, d.getJournal.getIssnLinking)) + + } + def toHostedByItem(input:String): HostedByItemType = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + + lazy val json: json4s.JValue = parse(input) + val c :Map[String,HostedByItemType] = json.extract[Map[String, HostedByItemType]] + c.values.head + } + + def explodeJournalInfo(input: DatasourceInfo): List[EntityInfo] = { + var lst : List[EntityInfo] = List() + if (input.getEissn != null && !input.getEissn.equals("")){ + lst = EntityInfo.newInstance(input.getId, input.getEissn, input.getOfficialname, input.getOpenAccess) :: lst + } + + lst + } + + 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/hostedbymap/hostedby_prepare_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val graphPath = parser.get("graphPath") + + val outputPath = parser.get("outputPath") + val hostedByMapPath = parser.get("hostedByMapPath") + + + implicit val formats = DefaultFormats + + + logger.info("Getting the Datasources") + + import spark.implicits._ + + //STEP1: leggere le DS e creare le entries {dsid, dsofficialname, issn, eissn, lissn, openaccess} + val datasourceInfoDataset: Dataset[DatasourceInfo] = prepareDatasourceInfo(spark, "$graphPath/datasource") + + //STEP2: leggere la hostedbymap e raggruppare per datasource id + val hostedByDataset = Aggregators.hostedByToSingleDSId(spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(toHostedByItem))) + + //STEP3: eseguire una join fra le datasource e la hostedby map (left) per settare se la datasource e' open access o no + //ed esplodere l'info della datasource per ogni journal id diverso da nullo + val join : Dataset[EntityInfo] = datasourceInfoDataset.joinWith(hostedByDataset, + datasourceInfoDataset.col("id").equalTo(hostedByDataset.col("id"), "left")) + .map(t2 => { + val dsi : DatasourceInfo = t2._1 + if(t2._2 != null){ + dsi.setOpenAccess(t2._2.openAccess) + } + dsi + }).flatMap(explodeJournalInfo) + + //STEP4: creare la mappa publication id issn, eissn, lissn esplosa + val resultInfoDataset:Dataset[EntityInfo] = prepareResultInfo(spark, "$graphPath/publication") + + //STEP5: join di join con resultInfo sul journal_id dal result con left + // e riduzione di tutti i result con lo stesso id in una unica entry + Aggregators.resultToSingleId(resultInfoDataset.joinWith(join, resultInfoDataset.col("journal_id").equalTo(join.col("journal_id")), "left") + .map(t2 => { + val res: EntityInfo = t2._1 + if(t2._2 != null ){ + val ds = t2._2 + res.setHb_id(ds.getId) + res.setOpenaccess(ds.getOpenaccess) + res.setName(ds.getName) + } + res + })).write.mode(SaveMode.Overwrite).option("compression", "gzip").json(outputPath) + + + + } + +} From 1695d45bd41a772319d357642df536cd8634faf2 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Fri, 30 Jul 2021 17:57:01 +0200 Subject: [PATCH 09/51] Hosted By Map - Test class to verify the preparation of the intermediate information --- .../oa/graph/hostedbymap/TestPrepare.scala | 53 +++++++++++++++++++ 1 file changed, 53 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala new file mode 100644 index 0000000000..f01e4f59fd --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala @@ -0,0 +1,53 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.DatasourceInfo +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, SparkSession} +import org.junit.jupiter.api.Assertions.{assertEquals, assertTrue} +import org.junit.jupiter.api.Test + +class TestPrepare extends java.io.Serializable{ + + @Test + def testPrepareDatasource():Unit = { + 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 ds :Dataset[DatasourceInfo]= SparkPrepareHostedByInfoToApply.prepareDatasourceInfo(spark, path) + + val mapper :ObjectMapper = new ObjectMapper() + + assertEquals(9, ds.count) + + assertEquals(8, ds.filter(hbi => !hbi.getIssn.equals("")).count) + assertEquals(5, ds.filter(hbi => !hbi.getEissn.equals("")).count) + assertEquals(0, ds.filter(hbi => !hbi.getLissn.equals("")).count) + + assertEquals(0, ds.filter(hbi => hbi.getIssn.equals("") && hbi.getEissn.equals("") && hbi.getLissn.equals("")).count) + + assertTrue(ds.filter(hbi => hbi.getIssn.equals("0212-8365")).count == 1) + assertTrue(ds.filter(hbi => hbi.getEissn.equals("2253-900X")).count == 1) + assertTrue(ds.filter(hbi => hbi.getIssn.equals("0212-8365") && hbi.getEissn.equals("2253-900X")).count == 1) + assertTrue(ds.filter(hbi => hbi.getIssn.equals("0212-8365") && hbi.getOfficialname.equals("Thémata")).count == 1) + assertTrue(ds.filter(hbi => hbi.getIssn.equals("0212-8365") && hbi.getId.equals("10|doajarticles::abbc9265bea9ff62776a1c39785af00c")).count == 1) + ds.foreach(hbi => assertTrue(hbi.getId.startsWith("10|"))) + ds.foreach(e => println(mapper.writeValueAsString(e))) + spark.close() + } + + @Test + def testPrepareHostedByMap():Unit = { + + } + + +} From ff1ce75e33e0f7cb2293c50e40b7ff83dd89bedb Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 2 Aug 2021 19:32:59 +0200 Subject: [PATCH 10/51] Hosted By Map - modification in the code to prepare the info needed to apply the HostedByMap. There is no need to join datasources with the hbm: all the information needed is in the hosted by map already --- .../SparkPrepareHostedByInfoToApply.scala | 104 +++++++++--------- 1 file changed, 55 insertions(+), 49 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala index 03ab09d8e8..7395b24506 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala @@ -3,7 +3,8 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DatasourceInfo, EntityInfo} -import eu.dnetlib.dhp.schema.oaf.{Datasource, Journal, Publication} + +import eu.dnetlib.dhp.schema.oaf.{Journal, Publication} import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Dataset, Encoder, Encoders, SaveMode, SparkSession} @@ -12,11 +13,13 @@ import org.json4s.DefaultFormats import org.json4s.jackson.JsonMethods.parse import org.slf4j.{Logger, LoggerFactory} + + object SparkPrepareHostedByInfoToApply { - implicit val mapEncoderDSInfo: Encoder[DatasourceInfo] = Encoders.kryo[DatasourceInfo] - implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.kryo[EntityInfo] + implicit val mapEncoderDSInfo: Encoder[DatasourceInfo] = Encoders.bean(classOf[DatasourceInfo]) + implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) def getList(id: String, j: Journal, name: String ) : List[EntityInfo] = { var lst:List[EntityInfo] = List() @@ -47,25 +50,12 @@ object SparkPrepareHostedByInfoToApply { } - - def prepareDatasourceInfo(spark:SparkSession, datasourcePath:String) : Dataset[DatasourceInfo] = { - implicit val mapEncoderDats: Encoder[Datasource] = Encoders.bean(classOf[Datasource]) - - val mapper = new ObjectMapper() - - val dd : Dataset[Datasource] = spark.read.textFile(datasourcePath) - .map(r => mapper.readValue(r, classOf[Datasource])) - - dd.filter(d => d.getJournal != null ).map(d => DatasourceInfo.newInstance(d.getId, d.getOfficialname.getValue, - d.getJournal.getIssnPrinted, d.getJournal.getIssnOnline, d.getJournal.getIssnLinking)) - - } - def toHostedByItem(input:String): HostedByItemType = { + def toEntityInfo(input:String): EntityInfo = { implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json: json4s.JValue = parse(input) val c :Map[String,HostedByItemType] = json.extract[Map[String, HostedByItemType]] - c.values.head + toEntityItem(c.keys.head, c.values.head) } def explodeJournalInfo(input: DatasourceInfo): List[EntityInfo] = { @@ -73,10 +63,49 @@ object SparkPrepareHostedByInfoToApply { if (input.getEissn != null && !input.getEissn.equals("")){ lst = EntityInfo.newInstance(input.getId, input.getEissn, input.getOfficialname, input.getOpenAccess) :: lst } + if (input.getLissn != null && !input.getLissn.equals("")){ + lst = EntityInfo.newInstance(input.getId, input.getLissn, input.getOfficialname, input.getOpenAccess) :: lst + } + if (input.getIssn != null && !input.getIssn.equals("")){ + lst = EntityInfo.newInstance(input.getId, input.getIssn, input.getOfficialname, input.getOpenAccess) :: lst + } lst } + def joinDsandHBM(left:Dataset[DatasourceInfo], right:Dataset[HostedByItemType]): Dataset[EntityInfo] = { + left.joinWith(right, + left.col("id").equalTo(right.col("id")), "left") + .map(t2 => { + val dsi : DatasourceInfo = t2._1 + if(t2._2 != null){ + val hbi : HostedByItemType = t2._2 + dsi.setOpenAccess(hbi.openAccess) + } + dsi + }).flatMap(explodeJournalInfo) + } + + def toEntityItem(journal_id: String , hbi: HostedByItemType): EntityInfo = { + + EntityInfo.newInstance(hbi.id, journal_id, hbi.officialname, hbi.openAccess) + + } + + def joinResHBM(res: Dataset[EntityInfo], hbm: Dataset[EntityInfo]): Dataset[EntityInfo] = { + Aggregators.resultToSingleId(res.joinWith(hbm, res.col("journal_id").equalTo(hbm.col("journal_id")), "left") + .map(t2 => { + val res: EntityInfo = t2._1 + if(t2._2 != null ){ + val ds = t2._2 + res.setHb_id(ds.getId) + res.setOpenaccess(ds.getOpenaccess) + res.setName(ds.getName) + } + res + })) + } + def main(args: Array[String]): Unit = { @@ -105,43 +134,20 @@ object SparkPrepareHostedByInfoToApply { import spark.implicits._ - //STEP1: leggere le DS e creare le entries {dsid, dsofficialname, issn, eissn, lissn, openaccess} - val datasourceInfoDataset: Dataset[DatasourceInfo] = prepareDatasourceInfo(spark, "$graphPath/datasource") - //STEP2: leggere la hostedbymap e raggruppare per datasource id - val hostedByDataset = Aggregators.hostedByToSingleDSId(spark.createDataset(spark.sparkContext.textFile(hostedByMapPath).map(toHostedByItem))) + //STEP1: leggere la hostedbymap e trasformarla in entity info + val hostedByInfo:Dataset[EntityInfo] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath)).map(toEntityInfo) - //STEP3: eseguire una join fra le datasource e la hostedby map (left) per settare se la datasource e' open access o no - //ed esplodere l'info della datasource per ogni journal id diverso da nullo - val join : Dataset[EntityInfo] = datasourceInfoDataset.joinWith(hostedByDataset, - datasourceInfoDataset.col("id").equalTo(hostedByDataset.col("id"), "left")) - .map(t2 => { - val dsi : DatasourceInfo = t2._1 - if(t2._2 != null){ - dsi.setOpenAccess(t2._2.openAccess) - } - dsi - }).flatMap(explodeJournalInfo) - - //STEP4: creare la mappa publication id issn, eissn, lissn esplosa + //STEP2: creare la mappa publication id issn, eissn, lissn esplosa val resultInfoDataset:Dataset[EntityInfo] = prepareResultInfo(spark, "$graphPath/publication") - //STEP5: join di join con resultInfo sul journal_id dal result con left - // e riduzione di tutti i result con lo stesso id in una unica entry - Aggregators.resultToSingleId(resultInfoDataset.joinWith(join, resultInfoDataset.col("journal_id").equalTo(join.col("journal_id")), "left") - .map(t2 => { - val res: EntityInfo = t2._1 - if(t2._2 != null ){ - val ds = t2._2 - res.setHb_id(ds.getId) - res.setOpenaccess(ds.getOpenaccess) - res.setName(ds.getName) - } - res - })).write.mode(SaveMode.Overwrite).option("compression", "gzip").json(outputPath) - + //STEP3: join resultInfo con hostedByInfo sul journal_id dal result con left + // e riduzione di tutti i result con lo stesso id in una unica entry con aggiunto l'id della datasource + joinResHBM(resultInfoDataset, hostedByInfo) + .write.mode(SaveMode.Overwrite).option("compression", "gzip").json(outputPath) } + } From 72df8f92320c7d0ddcecece72a8e3502f5b03022 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 2 Aug 2021 19:34:44 +0200 Subject: [PATCH 11/51] Hosted By Map - removed the aggregator for the datasource (it is no more needed) and added a new aggregator for the results. Changed also the hostedBYMap aggregator --- .../oa/graph/hostedbymap/Aggregators.scala | 36 +------------------ 1 file changed, 1 insertion(+), 35 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala index 8077efe302..af4ac45077 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala @@ -62,42 +62,7 @@ object Aggregators { override def outputEncoder: Encoder[(String,HostedByItemType)] = Encoders.tuple(Encoders.STRING,Encoders.product[HostedByItemType]) }.toColumn - def hostedByToSingleDSId(df: Dataset[ HostedByItemType]): Dataset[ HostedByItemType] = { - val transformedData : Dataset[HostedByItemType] = df - .groupByKey(_.id)(Encoders.STRING) - .agg(Aggregators.hostedByToDSAggregator) - .map{ - case (id:String , res: HostedByItemType) => res - }(Encoders.product[HostedByItemType]) - transformedData - } - - def hostedByToDSAggregator: 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 - } - if(!b1.id.equals("")){ - return HostedByItemType(b1.id, b1.officialname, b1.issn, b1.eissn, b1.lissn, b1.openAccess || b2.openAccess) - - } - return HostedByItemType(b2.id, b2.officialname, b2.issn, b2.eissn, 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 def resultToSingleIdAggregator: TypedColumn[EntityInfo, EntityInfo] = new Aggregator[EntityInfo, EntityInfo, EntityInfo]{ @@ -115,6 +80,7 @@ object Aggregators { } if(!b1.getHb_id.equals("")){ b1.setOpenaccess(b1.getOpenaccess || b2.getOpenaccess) + return b1 } b2.setOpenaccess(b1.getOpenaccess || b2.getOpenaccess) b2 From 1e859706a3516b8103342cbe875004a6c112d35b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 2 Aug 2021 19:35:23 +0200 Subject: [PATCH 12/51] Hosted By Map - Classes to apply the HBM to results and datasources --- .../SparkApplyHostedByMapToDatasource.scala | 72 +++++++++++++++ .../SparkApplyHostedByMapToResult.scala | 88 +++++++++++++++++++ 2 files changed, 160 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala new file mode 100644 index 0000000000..4ecea63f32 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala @@ -0,0 +1,72 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkApplyHostedByMapToResult.{applyHBtoPubs, getClass} +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{Datasource, Publication} +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} + +object SparkApplyHostedByMapToDatasource { + + def applyHBtoDats(join: Dataset[EntityInfo], dats: Dataset[Datasource]): Dataset[Datasource] = { + dats.joinWith(join, dats.col("id").equalTo(join.col("hb_id")), "left") + .map(t2 => { + val d: Datasource = t2._1 + if (t2._2 != null) { + if (d.getOpenairecompatibility.getClassid.equals(ModelConstants.UNKNOWN)) { + d.getOpenairecompatibility.setClassid("hostedBy") + d.getOpenairecompatibility.setClassname("collected from a compatible aggregator") + } + } + d + })(Encoders.bean((classOf[Datasource]))) + } + 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/hostedbymap/hostedby_apply_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val graphPath = parser.get("graphPath") + + val outputPath = parser.get("outputPath") + val workingPath = parser.get("workingPath") + + + implicit val formats = DefaultFormats + + + implicit val mapEncoderPubs: Encoder[Datasource] = Encoders.bean(classOf[Datasource]) + implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + val mapper = new ObjectMapper() + + val dats : Dataset[Datasource] = spark.read.textFile("$graphPath/datasource") + .map(r => mapper.readValue(r, classOf[Datasource])) + + val pinfo : Dataset[EntityInfo] = spark.read.textFile("$workingPath/preparedInfo") + .map(ei => mapper.readValue(ei, classOf[EntityInfo])) + + + + //c. dataset join risultato del passo prima di a per datasource id, gruppo per ds id e cambio compatibilita' se necessario + + applyHBtoDats(pinfo, dats).write.mode(SaveMode.Overwrite).option("compression","gzip").json(s"$graphPath/datasource") + } + + +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala new file mode 100644 index 0000000000..37afc319a2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala @@ -0,0 +1,88 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.application.ArgumentApplicationParser +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils +import eu.dnetlib.dhp.schema.oaf.{Datasource, Instance, OpenAccessRoute, Publication} +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 scala.collection.JavaConverters._ + +//a. publication join risultato del passo precedente su result id (left) setto la istanza (se piu' di una instance +// nel result => salto)con l'hosted by anche access right della instance se openaccess e' true + + +object SparkApplyHostedByMapToResult { + + def applyHBtoPubs(join: Dataset[EntityInfo], pubs: Dataset[Publication]) = { + pubs.joinWith(join, pubs.col("id").equalTo(join.col("id")), "left") + .map(t2 => { + val p: Publication = t2._1 + if (t2._2 != null) { + val ei: EntityInfo = t2._2 + val i = p.getInstance().asScala + if (i.size == 1) { + val inst: Instance = i(0) + + inst.getHostedby.setKey(ei.getHb_id) + inst.getHostedby.setValue(ei.getName) + if (ei.getOpenaccess) { + inst.setAccessright(OafMapperUtils.accessRight(ModelConstants.ACCESS_RIGHT_OPEN, "Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)) + inst.getAccessright.setOpenAccessRoute(OpenAccessRoute.hybrid) + } + + } + } + p + })(Encoders.bean(classOf[Publication])) + } + 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/hostedbymap/hostedby_apply_params.json"))) + parser.parseArgument(args) + val spark: SparkSession = + SparkSession + .builder() + .config(conf) + .appName(getClass.getSimpleName) + .master(parser.get("master")).getOrCreate() + + + val graphPath = parser.get("graphPath") + + val outputPath = parser.get("outputPath") + val workingPath = parser.get("workingPath") + + + implicit val formats = DefaultFormats + + + implicit val mapEncoderPubs: Encoder[Publication] = Encoders.bean(classOf[Publication]) + implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + val mapper = new ObjectMapper() + + val pubs : Dataset[Publication] = spark.read.textFile("$graphPath/publication") + .map(r => mapper.readValue(r, classOf[Publication])) + + val pinfo : Dataset[EntityInfo] = spark.read.textFile("$workingPath/preparedInfo") + .map(ei => mapper.readValue(ei, classOf[EntityInfo])) + + //a. publication join risultato del passo precedente su result id (left) setto la istanza (se piu' di una instance + // nel result => salto)con l'hosted by anche access right della instance se openaccess e' true + applyHBtoPubs(pinfo, pubs).write.mode(SaveMode.Overwrite).option("compression","gzip").json("$graphPath/publication") + + + + } + + +} From 90e91486e2cc63a51e51f5e2412ad3ff7c49ba19 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 2 Aug 2021 19:35:52 +0200 Subject: [PATCH 13/51] Hosted By Map - test class to verify each step in the preparation process --- .../oa/graph/hostedbymap/TestPrepare.scala | 142 +++++++++++++++--- 1 file changed, 124 insertions(+), 18 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala index f01e4f59fd..efd598fef7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestPrepare.scala @@ -1,16 +1,31 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap import com.fasterxml.jackson.databind.ObjectMapper -import eu.dnetlib.dhp.oa.graph.hostedbymap.model.DatasourceInfo +import eu.dnetlib.dhp.oa.graph.hostedbymap.SparkPrepareHostedByInfoToApply.{joinResHBM, prepareResultInfo, toEntityInfo} +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo +import eu.dnetlib.dhp.schema.oaf.{Datasource, OpenAccessRoute, Publication} +import javax.management.openmbean.OpenMBeanAttributeInfo import org.apache.spark.SparkConf -import org.apache.spark.sql.{Dataset, SparkSession} +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.json4s +import org.json4s.DefaultFormats +import eu.dnetlib.dhp.schema.common.ModelConstants import org.junit.jupiter.api.Assertions.{assertEquals, assertTrue} import org.junit.jupiter.api.Test class TestPrepare extends java.io.Serializable{ + def getString(input:HostedByItemType):String = { + + import org.json4s.jackson.Serialization.write + implicit val formats = DefaultFormats + + write(input) + } + + @Test - def testPrepareDatasource():Unit = { + def testHostedByMaptoEntityInfo() : Unit = { val conf = new SparkConf() conf.setMaster("local[*]") conf.set("spark.driver.host", "localhost") @@ -20,34 +35,125 @@ class TestPrepare extends java.io.Serializable{ .appName(getClass.getSimpleName) .config(conf) .getOrCreate() - val path = getClass.getResource("datasource.json").getPath + val hbm = getClass.getResource("hostedbymap.json").getPath - val ds :Dataset[DatasourceInfo]= SparkPrepareHostedByInfoToApply.prepareDatasourceInfo(spark, path) - val mapper :ObjectMapper = new ObjectMapper() + import spark.implicits._ - assertEquals(9, ds.count) + val mapper:ObjectMapper = new ObjectMapper() - assertEquals(8, ds.filter(hbi => !hbi.getIssn.equals("")).count) - assertEquals(5, ds.filter(hbi => !hbi.getEissn.equals("")).count) - assertEquals(0, ds.filter(hbi => !hbi.getLissn.equals("")).count) + implicit val mapEncoderDSInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) - assertEquals(0, ds.filter(hbi => hbi.getIssn.equals("") && hbi.getEissn.equals("") && hbi.getLissn.equals("")).count) + val ds :Dataset[EntityInfo] = spark.createDataset(spark.sparkContext.textFile(hbm)).map(toEntityInfo) - assertTrue(ds.filter(hbi => hbi.getIssn.equals("0212-8365")).count == 1) - assertTrue(ds.filter(hbi => hbi.getEissn.equals("2253-900X")).count == 1) - assertTrue(ds.filter(hbi => hbi.getIssn.equals("0212-8365") && hbi.getEissn.equals("2253-900X")).count == 1) - assertTrue(ds.filter(hbi => hbi.getIssn.equals("0212-8365") && hbi.getOfficialname.equals("Thémata")).count == 1) - assertTrue(ds.filter(hbi => hbi.getIssn.equals("0212-8365") && hbi.getId.equals("10|doajarticles::abbc9265bea9ff62776a1c39785af00c")).count == 1) - ds.foreach(hbi => assertTrue(hbi.getId.startsWith("10|"))) ds.foreach(e => println(mapper.writeValueAsString(e))) + + assertEquals(20, ds.count) spark.close() } @Test - def testPrepareHostedByMap():Unit = { + def testPublicationtoEntityInfo() : Unit = { + 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("publication.json").getPath + val mapper:ObjectMapper = new ObjectMapper() + + implicit val mapEncoderDSInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + + val ds :Dataset[EntityInfo] = prepareResultInfo(spark, path) + + ds.foreach(e => println(mapper.writeValueAsString(e))) + + assertEquals(2, ds.count) + + assertEquals("50|4dc99724cf04::ed1ba83e1add6ce292433729acd8b0d9", ds.filter(ei => ei.getJournal_id.equals("1728-5852")).first().getId) + assertEquals("50|4dc99724cf04::ed1ba83e1add6ce292433729acd8b0d9", ds.filter(ei => ei.getJournal_id.equals("0001-396X")).first().getId) + + spark.close() + } + + @Test + def testJoinResHBM (): Unit = { + 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 pub = getClass.getResource("iteminfofrompublication").getPath + val hbm = getClass.getResource("iteminfofromhostedbymap.json").getPath + + val mapper:ObjectMapper = new ObjectMapper() + + implicit val mapEncoderDSInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + + val pub_ds :Dataset[EntityInfo] = spark.read.textFile(pub).map(p => mapper.readValue(p, classOf[EntityInfo])) + val hbm_ds :Dataset[EntityInfo] = spark.read.textFile(hbm).map(p => mapper.readValue(p, classOf[EntityInfo])) + + val ds: Dataset[EntityInfo] = joinResHBM(pub_ds, hbm_ds) + + assertEquals(1, ds.count) + + val ei:EntityInfo = ds.first() + + assertEquals("50|4dc99724cf04::ed1ba83e1add6ce292433729acd8b0d9", ei.getId) + assertEquals("10|issn___print::e4b6d6d978f67520f6f37679a98c5735", ei.getHb_id) + assertEquals("0001-396X", ei.getJournal_id) + assertEquals("Academic Therapy", ei.getName) + assertTrue(!ei.getOpenaccess) + + spark.close() + } + + @Test + def testJoinResHBM2 (): Unit = { + 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 pub = getClass.getResource("iteminfofrompublication2").getPath + val hbm = getClass.getResource("iteminfofromhostedbymap2.json").getPath + + val mapper:ObjectMapper = new ObjectMapper() + + implicit val mapEncoderDSInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + + val pub_ds :Dataset[EntityInfo] = spark.read.textFile(pub).map(p => mapper.readValue(p, classOf[EntityInfo])) + val hbm_ds :Dataset[EntityInfo] = spark.read.textFile(hbm).map(p => mapper.readValue(p, classOf[EntityInfo])) + + val ds: Dataset[EntityInfo] = joinResHBM(pub_ds, hbm_ds) + + assertEquals(1, ds.count) + + val ei:EntityInfo = ds.first() + + assertEquals("50|4dc99724cf04::ed1ba83e1add6ce292433729acd8b0d9", ei.getId) + assertEquals("10|issn___print::e4b6d6d978f67520f6f37679a98c5735", ei.getHb_id) + assertEquals("Academic Therapy", ei.getName) + assertTrue(ei.getOpenaccess) + + ds.foreach(e => println(mapper.writeValueAsString(e))) + + spark.close() } + } From ee7ccb98dc716313b620dc47d02b1bb277632246 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 2 Aug 2021 19:36:18 +0200 Subject: [PATCH 14/51] Hosted By Map - test class to verify the application of the hbm to results and datasource --- .../dhp/oa/graph/hostedbymap/TestApply.scala | 134 ++++++++++++++++++ 1 file changed, 134 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala new file mode 100644 index 0000000000..b78eb978bf --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala @@ -0,0 +1,134 @@ +package eu.dnetlib.dhp.oa.graph.hostedbymap + +import com.fasterxml.jackson.databind.ObjectMapper +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo +import eu.dnetlib.dhp.schema.common.ModelConstants +import eu.dnetlib.dhp.schema.oaf.{Datasource, OpenAccessRoute, Publication} +import org.apache.spark.SparkConf +import org.apache.spark.sql.{Dataset, Encoder, Encoders, SparkSession} +import org.junit.jupiter.api.Assertions.{assertEquals, assertTrue} +import org.junit.jupiter.api.Test + +class TestApply extends java.io.Serializable{ + + @Test + def testApplyOnResult (): Unit = { + 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 pub = getClass.getResource("publication.json").getPath + val hbm = getClass.getResource("preparedInfo.json").getPath + + val mapper:ObjectMapper = new ObjectMapper() + + implicit val mapEncoderDSInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + implicit val mapEncoderPubInfo: Encoder[Publication] = Encoders.bean(classOf[Publication]) + + + val pub_ds :Dataset[Publication] = spark.read.textFile(pub).map(p => mapper.readValue(p, classOf[Publication])) + val hbm_ds :Dataset[EntityInfo] = spark.read.textFile(hbm).map(p => mapper.readValue(p, classOf[EntityInfo])) + + + assertEquals(13, pub_ds.count()) + + val ds:Dataset[Publication] = SparkApplyHostedByMapToResult.applyHBtoPubs(hbm_ds, pub_ds) + + assertEquals(13, ds.count) + + val temp: Dataset[(Publication, Publication)] = pub_ds.joinWith(ds, pub_ds.col("id").equalTo(ds.col("id")), "left") + assertEquals(13, temp.count()) + temp.foreach(t2 => { + val pb : Publication = t2._1 + val pa : Publication = t2._2 + assertEquals(1, pa.getInstance().size()) + assertEquals(1, pb.getInstance().size()) + assertTrue(t2._1.getId.equals(t2._2.getId)) + if(pb.getId.equals("50|4dc99724cf04::ed1ba83e1add6ce292433729acd8b0d9")){ + assertTrue(pa.getInstance().get(0).getHostedby.getKey.equals("10|issn___print::e4b6d6d978f67520f6f37679a98c5735")) + assertTrue(pa.getInstance().get(0).getHostedby.getValue.equals("Academic Therapy")) + assertTrue(pa.getInstance().get(0).getAccessright.getClassid.equals("OPEN")) + assertTrue(pa.getInstance().get(0).getAccessright.getClassname.equals("Open Access")) + assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.hybrid)) + + + assertTrue(pb.getInstance().get(0).getHostedby.getKey.equals("10|openaire____::0b74b6a356bbf23c245f9ae9a748745c")) + assertTrue(pb.getInstance().get(0).getHostedby.getValue.equals("Revistas de investigación Universidad Nacional Mayor de San Marcos")) + assertTrue(pb.getInstance().get(0).getAccessright.getClassname.equals("Open Access")) + assertTrue(pb.getInstance().get(0).getAccessright.getClassid.equals("OPEN")) + assertTrue(pb.getInstance().get(0).getAccessright.getOpenAccessRoute == null) + + }else{ + assertTrue(pa.getInstance().get(0).getHostedby.getKey.equals(pb.getInstance().get(0).getHostedby.getKey)) + assertTrue(pa.getInstance().get(0).getHostedby.getValue.equals(pb.getInstance().get(0).getHostedby.getValue)) + assertTrue(pa.getInstance().get(0).getAccessright.getClassid.equals(pb.getInstance().get(0).getAccessright.getClassid)) + assertTrue(pa.getInstance().get(0).getAccessright.getClassname.equals(pb.getInstance().get(0).getAccessright.getClassname)) + assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute == pb.getInstance().get(0).getAccessright.getOpenAccessRoute) + + } + }) + + spark.close() + } + + + @Test + def testApplyOnDatasource():Unit = { + 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 dats = getClass.getResource("datasource.json").getPath + val hbm = getClass.getResource("preparedInfo2.json").getPath + + val mapper:ObjectMapper = new ObjectMapper() + + implicit val mapEncoderDSInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + implicit val mapEncoderPubInfo: Encoder[Datasource] = Encoders.bean(classOf[Datasource]) + + + val dats_ds :Dataset[Datasource] = spark.read.textFile(dats).map(p => mapper.readValue(p, classOf[Datasource])) + val hbm_ds :Dataset[EntityInfo] = spark.read.textFile(hbm).map(p => mapper.readValue(p, classOf[EntityInfo])) + + + assertEquals(10, dats_ds.count()) + + val ds:Dataset[Datasource] = SparkApplyHostedByMapToDatasource.applyHBtoDats(hbm_ds, dats_ds) + + assertEquals(10, ds.count) + + val temp: Dataset[(Datasource, Datasource)] = dats_ds.joinWith(ds, dats_ds.col("id").equalTo(ds.col("id")), "left") + assertEquals(10, temp.count()) + temp.foreach(t2 => { + val pb : Datasource = t2._1 + val pa : Datasource = t2._2 + assertTrue(t2._1.getId.equals(t2._2.getId)) + if(pb.getId.equals("10|doajarticles::0ab37b7620eb9a73ac95d3ca4320c97d")){ + assertTrue(pa.getOpenairecompatibility().getClassid.equals("hostedBy")) + assertTrue(pa.getOpenairecompatibility().getClassname.equals("collected from a compatible aggregator")) + + assertTrue(pb.getOpenairecompatibility().getClassid.equals(ModelConstants.UNKNOWN)) + + + }else{ + assertTrue(pa.getOpenairecompatibility().getClassid.equals(pb.getOpenairecompatibility.getClassid)) + assertTrue(pa.getOpenairecompatibility().getClassname.equals(pb.getOpenairecompatibility.getClassid)) + + } + }) + + spark.close() + + } + +} From 17292c6641439f175b41e665422dea25a19d44f7 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 2 Aug 2021 19:37:08 +0200 Subject: [PATCH 15/51] Hosted By Map - resources for testing purposes --- .../dhp/oa/graph/hostedbymap/datasource.json | 4 ++-- .../oa/graph/hostedbymap/datasourceinfo.json | 9 +++++++++ .../graph/hostedbymap/hostedbyitemtype.json | 17 ++++++++++++++++ .../dhp/oa/graph/hostedbymap/hostedbymap.json | 20 +++++++++++++++++++ .../hostedbymap/iteminfofromhostedbymap.json | 20 +++++++++++++++++++ .../hostedbymap/iteminfofromhostedbymap2.json | 20 +++++++++++++++++++ .../graph/hostedbymap/iteminfofrompublication | 2 ++ .../hostedbymap/iteminfofrompublication2 | 2 ++ .../oa/graph/hostedbymap/preparedInfo.json | 1 + .../oa/graph/hostedbymap/preparedInfo2.json | 2 ++ .../dhp/oa/graph/hostedbymap/publication.json | 13 ++++++++++++ 11 files changed, 108 insertions(+), 2 deletions(-) create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/datasourceinfo.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedbyitemtype.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedbymap.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/iteminfofromhostedbymap.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/iteminfofromhostedbymap2.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/iteminfofrompublication create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/iteminfofrompublication2 create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/preparedInfo.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/preparedInfo2.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/publication.json 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 index 4467c702f6..5eb41bff5d 100644 --- 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 @@ -1,5 +1,5 @@ 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An automatic gamma spectrometer for activation analysis has been developed at the Technical Research Centre of Finland. The on-line system comprises a sample changer for up to 120 samples, detector, multichannel analyzer, microcomputer programmed with Basic language and input/output devices.

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Erzählt wird in TEOREMA die Geschichte einer zu Beginn des Films anscheinend intakten Familie, die sich durch die Begegnung mit einem Unbekannten der eigenen Leere bewusst wird und auseinanderfällt. Der Film endet mit dem Schrei eines der Protagonisten, der hier jedoch weniger ein neues Leben bedeutet, als vielmehr eine Reaktion auf die repressiven und normativen Mechanismen der Gesellschaft. Hanekes Filme LEMMINGE, TEIL II und DER SIEBENTE KONTINENT gehen jeweils unter-schiedlich von einer vergleichbaren Prämisse einer leeren Familie aus. Doch während die Schreie in den LEMMINGEN immer lauter werden, verstummen sie im SIEBENTEN KONTINENT schließlich. In allen benannten Filmen hat das Werk Francis Bacons eine besondere Rolle gespielt und wurde entweder explizit (TEOREMA, LEMMINGE II) oder implizit (DER SIEBENTE KONTINENT) thematisiert. Der Vortrag geht den Bildern des (stummen) Schreis in den genannten Filmen nach."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|57a035e5b1ae::023bc0883fb1075fe0a86e829b6c5d97","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2014-01-01"},"hostedby":{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"},"instancetype":{"classid":"0004","classname":"Conference object","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"pid":[],"refereed":{"classid":"0000","classname":"Unknown","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["https://www.bib.irb.hr/848053"]}],"language":{"classid":"deu/ger","classname":"German","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1627813203778,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"https%3A%2F%2Fbib.irb.hr%2Foai2%2F","datestamp":"2016-12-06T18:47:39Z","harvestDate":"2021-07-11T01:23:38.842Z","identifier":"848053","metadataNamespace":""}},"originalId":["848053","50|57a035e5b1ae::023bc0883fb1075fe0a86e829b6c5d97"],"pid":[],"relevantdate":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"issued","classname":"issued","schemeid":"dnet:dataCite_date","schemename":"dnet:dataCite_date"},"value":"2014-01-01"}],"resourcetype":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[],"subject":[],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","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":"\"Teorema\" von Pier Paolo Pasolini oder: Ein Schrei auf Francis Bacons Spuren"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","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":"\"Teorema\" by Pier Paolo Pasolini"}]} \ No newline at end of file From 327cddde336a2a590efeba3a76febb1cec36711b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 3 Aug 2021 10:44:13 +0200 Subject: [PATCH 16/51] Hosted By Map - refactoring --- .../graph/hostedbymap/model/EntityInfo.java | 97 +++++++++---------- 1 file changed, 48 insertions(+), 49 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/EntityInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/EntityInfo.java index 7bf9d05982..1facaa7923 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/EntityInfo.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/EntityInfo.java @@ -1,69 +1,68 @@ + package eu.dnetlib.dhp.oa.graph.hostedbymap.model; import java.io.Serializable; public class EntityInfo implements Serializable { - private String id; - private String journal_id; - private String name; - private Boolean openaccess; - private String hb_id; + private String id; + private String journal_id; + private String name; + private Boolean openaccess; + private String hb_id; + public String getId() { + return id; + } + public void setId(String id) { + this.id = id; + } - public String getId() { - return id; - } + public String getJournal_id() { + return journal_id; + } - public void setId(String id) { - this.id = id; - } + public void setJournal_id(String journal_id) { + this.journal_id = journal_id; + } - public String getJournal_id() { - return journal_id; - } + public String getName() { + return name; + } - public void setJournal_id(String journal_id) { - this.journal_id = journal_id; - } + public void setName(String name) { + this.name = name; + } - public String getName() { - return name; - } + public Boolean getOpenaccess() { + return openaccess; + } - public void setName(String name) { - this.name = name; - } + public void setOpenaccess(Boolean openaccess) { + this.openaccess = openaccess; + } - public Boolean getOpenaccess() { - return openaccess; - } + public String getHb_id() { + return hb_id; + } - public void setOpenaccess(Boolean openaccess) { - this.openaccess = openaccess; - } + public void setHb_id(String hb_id) { + this.hb_id = hb_id; + } - public String getHb_id() { - return hb_id; - } + public static EntityInfo newInstance(String id, String j_id, String name) { + return newInstance(id, j_id, name, false); - public void setHb_id(String hb_id) { - this.hb_id = hb_id; - } + } - public static EntityInfo newInstance(String id, String j_id, String name){ - return newInstance(id, j_id, name, false); + public static EntityInfo newInstance(String id, String j_id, String name, Boolean openaccess) { + EntityInfo pi = new EntityInfo(); + pi.id = id; + pi.journal_id = j_id; + pi.name = name; + pi.openaccess = openaccess; + pi.hb_id = ""; + return pi; - } - - public static EntityInfo newInstance(String id, String j_id, String name, Boolean openaccess){ - EntityInfo pi = new EntityInfo(); - pi.id = id; - pi.journal_id = j_id; - pi.name = name; - pi.openaccess = openaccess; - pi.hb_id = ""; - return pi; - - } + } } From 461b8a29a0e52d92cb12aaec7e481844f9124c51 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 3 Aug 2021 10:46:51 +0200 Subject: [PATCH 17/51] removed not needed class --- .../hostedbymap/model/DatasourceInfo.java | 72 ------------------- 1 file changed, 72 deletions(-) delete mode 100644 dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DatasourceInfo.java diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DatasourceInfo.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DatasourceInfo.java deleted file mode 100644 index f5ac8f70c5..0000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/model/DatasourceInfo.java +++ /dev/null @@ -1,72 +0,0 @@ -package eu.dnetlib.dhp.oa.graph.hostedbymap.model; - -import java.io.Serializable; - -public class DatasourceInfo implements Serializable { - private String id; - private String officialname; - private String issn; - private String eissn; - private String lissn; - private Boolean openAccess; - - public String getId() { - return id; - } - - public void setId(String id) { - this.id = id; - } - - public String getOfficialname() { - return officialname; - } - - public void setOfficialname(String officialname) { - this.officialname = officialname; - } - - 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 getLissn() { - return lissn; - } - - public void setLissn(String lissn) { - this.lissn = lissn; - } - - public Boolean getOpenAccess() { - return openAccess; - } - - public void setOpenAccess(Boolean openAccess) { - this.openAccess = openAccess; - } - - public static DatasourceInfo newInstance(String id, String officialname, String issn, String eissn, String lissn){ - DatasourceInfo di = new DatasourceInfo(); - di.id = id; - di.officialname = officialname; - di.issn = (issn != null) ? issn : "" ; - di.eissn = (eissn != null) ? eissn:""; - di.lissn = (lissn != null) ? lissn : ""; - di.openAccess = false; - - return di; - } -} From 9831725073e21ed89e014072c92cc0fc57642cee Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 3 Aug 2021 11:02:17 +0200 Subject: [PATCH 18/51] Hosted By Map - remove from workflow a step not needed. The hbm will be take care also of the integration of the unibi list of gold openaccess journals --- .../dhp/doiboost/preprocess/oozie_app/workflow.xml | 13 ------------- 1 file changed, 13 deletions(-) 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 4de1a21854..de433b038c 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 @@ -63,7 +63,6 @@ - ${wf:conf('resumeFrom') eq 'DownloadGoldIssn'} ${wf:conf('resumeFrom') eq 'UnpackCrossrefEntries'} ${wf:conf('resumeFrom') eq 'GenerateCrossrefDataset'} ${wf:conf('resumeFrom') eq 'ResetMagWorkingPath'} @@ -77,18 +76,6 @@ Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - - - eu.dnetlib.doiboost.GetCSV - --hdfsNameNode${nameNode} - --fileURL${unibiGoldIssnFileURL} - --hdfsPath${hdfsPath} - --classForNameeu.dnetlib.doiboost.UnibiGoldModel - - - - - From a7bf314fd2a8c0fb1075eb2738023e7d802d0364 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:13:30 +0200 Subject: [PATCH 19/51] Hosted By Map - added new aggregator to get just one result per datasource id --- .../oa/graph/hostedbymap/Aggregators.scala | 36 +++++++++++++++++++ 1 file changed, 36 insertions(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala index af4ac45077..8198b197aa 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/Aggregators.scala @@ -103,4 +103,40 @@ object Aggregators { transformedData } + def datasourceToSingleIdAggregator: TypedColumn[EntityInfo, EntityInfo] = new Aggregator[EntityInfo, EntityInfo, EntityInfo]{ + override def zero: EntityInfo = EntityInfo.newInstance("","","") + + override def reduce(b: EntityInfo, a:EntityInfo): EntityInfo = { + return merge(b, a) + } + override def merge(b1: EntityInfo, b2: EntityInfo): EntityInfo = { + if (b1 == null){ + return b2 + } + if(b2 == null){ + return b1 + } + if(!b1.getHb_id.equals("")){ + return b1 + } + b2 + + } + override def finish(reduction: EntityInfo): EntityInfo = reduction + override def bufferEncoder: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + + override def outputEncoder: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) + }.toColumn + + + def datasourceToSingleId(df:Dataset[EntityInfo]): Dataset[EntityInfo] = { + val transformedData : Dataset[EntityInfo] = df + .groupByKey(_.getHb_id)(Encoders.STRING) + .agg(Aggregators.datasourceToSingleIdAggregator) + .map{ + case (id:String , res: EntityInfo) => res + }(Encoders.bean(classOf[EntityInfo])) + + transformedData + } } From 8f7623e77afe2edce3681a81a0283f007f733c9d Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:14:20 +0200 Subject: [PATCH 20/51] Hosted By Map - refactoring and application of the new aggregator --- .../SparkApplyHostedByMapToDatasource.scala | 12 +++++------- 1 file changed, 5 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala index 4ecea63f32..fad313f1cd 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala @@ -45,7 +45,7 @@ object SparkApplyHostedByMapToDatasource { val graphPath = parser.get("graphPath") val outputPath = parser.get("outputPath") - val workingPath = parser.get("workingPath") + val preparedInfoPath = parser.get("preparedInfoPath") implicit val formats = DefaultFormats @@ -55,17 +55,15 @@ object SparkApplyHostedByMapToDatasource { implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) val mapper = new ObjectMapper() - val dats : Dataset[Datasource] = spark.read.textFile("$graphPath/datasource") + val dats : Dataset[Datasource] = spark.read.textFile(graphPath + "/datasource") .map(r => mapper.readValue(r, classOf[Datasource])) - val pinfo : Dataset[EntityInfo] = spark.read.textFile("$workingPath/preparedInfo") - .map(ei => mapper.readValue(ei, classOf[EntityInfo])) - - + val pinfo : Dataset[EntityInfo] = Aggregators.datasourceToSingleId( spark.read.textFile(preparedInfoPath) + .map(ei => mapper.readValue(ei, classOf[EntityInfo]))) //c. dataset join risultato del passo prima di a per datasource id, gruppo per ds id e cambio compatibilita' se necessario - applyHBtoDats(pinfo, dats).write.mode(SaveMode.Overwrite).option("compression","gzip").json(s"$graphPath/datasource") + applyHBtoDats(pinfo, dats).write.mode(SaveMode.Overwrite).option("compression","gzip").json(outputPath) } From 8ba8c77f92a82104076649fb3ba4fa80d13fd449 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:14:57 +0200 Subject: [PATCH 21/51] Hosted By Map - refactoring --- .../hostedbymap/SparkApplyHostedByMapToResult.scala | 9 ++++----- 1 file changed, 4 insertions(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala index 37afc319a2..312513285c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala @@ -29,7 +29,6 @@ object SparkApplyHostedByMapToResult { val i = p.getInstance().asScala if (i.size == 1) { val inst: Instance = i(0) - inst.getHostedby.setKey(ei.getHb_id) inst.getHostedby.setValue(ei.getName) if (ei.getOpenaccess) { @@ -60,7 +59,7 @@ object SparkApplyHostedByMapToResult { val graphPath = parser.get("graphPath") val outputPath = parser.get("outputPath") - val workingPath = parser.get("workingPath") + val preparedInfoPath = parser.get("preparedInfoPath") implicit val formats = DefaultFormats @@ -70,15 +69,15 @@ object SparkApplyHostedByMapToResult { implicit val mapEncoderEinfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) val mapper = new ObjectMapper() - val pubs : Dataset[Publication] = spark.read.textFile("$graphPath/publication") + val pubs : Dataset[Publication] = spark.read.textFile(graphPath + "/publication") .map(r => mapper.readValue(r, classOf[Publication])) - val pinfo : Dataset[EntityInfo] = spark.read.textFile("$workingPath/preparedInfo") + val pinfo : Dataset[EntityInfo] = spark.read.textFile(preparedInfoPath) .map(ei => mapper.readValue(ei, classOf[EntityInfo])) //a. publication join risultato del passo precedente su result id (left) setto la istanza (se piu' di una instance // nel result => salto)con l'hosted by anche access right della instance se openaccess e' true - applyHBtoPubs(pinfo, pubs).write.mode(SaveMode.Overwrite).option("compression","gzip").json("$graphPath/publication") + applyHBtoPubs(pinfo, pubs).write.mode(SaveMode.Overwrite).option("compression","gzip").json(outputPath) From 1e952cccf644a27180684b62851171ccdfd313d3 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:15:43 +0200 Subject: [PATCH 22/51] Hosted By Map - refactoring and deletion of not needed methods --- .../SparkPrepareHostedByInfoToApply.scala | 35 ++----------------- 1 file changed, 3 insertions(+), 32 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala index 7395b24506..d342d57b07 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala @@ -2,7 +2,7 @@ package eu.dnetlib.dhp.oa.graph.hostedbymap import com.fasterxml.jackson.databind.ObjectMapper import eu.dnetlib.dhp.application.ArgumentApplicationParser -import eu.dnetlib.dhp.oa.graph.hostedbymap.model.{DatasourceInfo, EntityInfo} +import eu.dnetlib.dhp.oa.graph.hostedbymap.model.EntityInfo import eu.dnetlib.dhp.schema.oaf.{Journal, Publication} import org.apache.commons.io.IOUtils @@ -17,8 +17,6 @@ import org.slf4j.{Logger, LoggerFactory} object SparkPrepareHostedByInfoToApply { - - implicit val mapEncoderDSInfo: Encoder[DatasourceInfo] = Encoders.bean(classOf[DatasourceInfo]) implicit val mapEncoderPInfo: Encoder[EntityInfo] = Encoders.bean(classOf[EntityInfo]) def getList(id: String, j: Journal, name: String ) : List[EntityInfo] = { @@ -58,33 +56,6 @@ object SparkPrepareHostedByInfoToApply { toEntityItem(c.keys.head, c.values.head) } - def explodeJournalInfo(input: DatasourceInfo): List[EntityInfo] = { - var lst : List[EntityInfo] = List() - if (input.getEissn != null && !input.getEissn.equals("")){ - lst = EntityInfo.newInstance(input.getId, input.getEissn, input.getOfficialname, input.getOpenAccess) :: lst - } - if (input.getLissn != null && !input.getLissn.equals("")){ - lst = EntityInfo.newInstance(input.getId, input.getLissn, input.getOfficialname, input.getOpenAccess) :: lst - } - if (input.getIssn != null && !input.getIssn.equals("")){ - lst = EntityInfo.newInstance(input.getId, input.getIssn, input.getOfficialname, input.getOpenAccess) :: lst - } - - lst - } - - def joinDsandHBM(left:Dataset[DatasourceInfo], right:Dataset[HostedByItemType]): Dataset[EntityInfo] = { - left.joinWith(right, - left.col("id").equalTo(right.col("id")), "left") - .map(t2 => { - val dsi : DatasourceInfo = t2._1 - if(t2._2 != null){ - val hbi : HostedByItemType = t2._2 - dsi.setOpenAccess(hbi.openAccess) - } - dsi - }).flatMap(explodeJournalInfo) - } def toEntityItem(journal_id: String , hbi: HostedByItemType): EntityInfo = { @@ -123,7 +94,7 @@ object SparkPrepareHostedByInfoToApply { val graphPath = parser.get("graphPath") - val outputPath = parser.get("outputPath") + val outputPath = parser.get("preparedInfoPath") val hostedByMapPath = parser.get("hostedByMapPath") @@ -139,7 +110,7 @@ object SparkPrepareHostedByInfoToApply { val hostedByInfo:Dataset[EntityInfo] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath)).map(toEntityInfo) //STEP2: creare la mappa publication id issn, eissn, lissn esplosa - val resultInfoDataset:Dataset[EntityInfo] = prepareResultInfo(spark, "$graphPath/publication") + val resultInfoDataset:Dataset[EntityInfo] = prepareResultInfo(spark, graphPath + "/publication") //STEP3: join resultInfo con hostedByInfo sul journal_id dal result con left // e riduzione di tutti i result con lo stesso id in una unica entry con aggiunto l'id della datasource From eccf3851b0352b557a4cce3dbd90d0fcf8ee3408 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:16:30 +0200 Subject: [PATCH 23/51] Hosted By Map - refactoring --- .../dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala index ca5e82a4a1..de41ebf28f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkProduceHostedByMap.scala @@ -23,10 +23,6 @@ object SparkProduceHostedByMap { implicit val tupleForJoinEncoder: Encoder[(String, HostedByItemType)] = Encoders.tuple(Encoders.STRING, Encoders.product[HostedByItemType]) - - - - def toHostedByItemType(input: ((HostedByInfo, HostedByInfo), HostedByInfo)) : HostedByItemType = { val openaire: HostedByInfo = input._1._1 val doaj: HostedByInfo = input._1._2 @@ -217,7 +213,7 @@ object SparkProduceHostedByMap { .union(doajHostedByDataset(spark, workingDirPath + "/doaj")) .flatMap(hbi => toList(hbi))).filter(hbi => hbi._2.id.startsWith("10|")) .map(hbi => toHostedByMap(hbi))(Encoders.STRING) - .rdd.saveAsTextFile(outputPath + "/hostedByMap", classOf[GzipCodec]) + .rdd.saveAsTextFile(outputPath , classOf[GzipCodec]) } From 67ba4c40e05bc90da931f7a621e11038849453db Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:17:28 +0200 Subject: [PATCH 24/51] Hosted By Map - added parameter resources --- .../hostedbymap/hostedby_apply_params.json | 36 ++++++++++++++++++ .../hostedbymap/hostedby_prepare_params.json | 37 +++++++++++++++++++ 2 files changed, 73 insertions(+) create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_apply_params.json create mode 100644 dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_prepare_params.json diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_apply_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_apply_params.json new file mode 100644 index 0000000000..e34398290a --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_apply_params.json @@ -0,0 +1,36 @@ + +[ + + { + "paramName":"pip", + "paramLongName":"preparedInfoPath", + "paramDescription": "the path where to find the pre-processed data for unibi gold list and doj artciles", + "paramRequired": true + }, + + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": true + }, + + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": true + }, + { + "paramName": "out", + "paramLongName": "outputPath", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": true + } +] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_prepare_params.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_prepare_params.json new file mode 100644 index 0000000000..9809d71b56 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/hostedby_prepare_params.json @@ -0,0 +1,37 @@ + +[ + + { + "paramName":"hbmp", + "paramLongName":"hostedByMapPath", + "paramDescription": "the path to the datasource ", + "paramRequired": true + }, + + { + "paramName":"pip", + "paramLongName":"preparedInfoPath", + "paramDescription": "the path where to find the pre-processed data for unibi gold list and doj artciles", + "paramRequired": true + }, + + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + }, + { + "paramName": "m", + "paramLongName": "master", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": true + }, + + { + "paramName": "gp", + "paramLongName": "graphPath", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": true + } +] From e94ae0b1de11f31dad6367605538371d9fe13d6b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:18:11 +0200 Subject: [PATCH 25/51] Hosted By Map - extention of the workflow to consider also the application of the map to publications and datasources --- .../graph/hostedbymap/oozie_app/workflow.xml | 106 ++++++++++++++++-- 1 file changed, 99 insertions(+), 7 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml index ecf6c3b316..30e500da3c 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml @@ -9,6 +9,10 @@ outputPath the output path + + hostedByMapPath + the output path + sparkDriverMemory memory for driver process @@ -65,23 +69,30 @@ - + + + + + ${wf:conf('resumeFrom') eq 'ProduceHBM'} + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] - + - - + + - @@ -134,13 +145,94 @@ --datasourcePath${sourcePath}/datasource --workingPath${workingDir} - --outputPath${outputPath} + --outputPath${hostedByMapPath} --masteryarn-cluster - + + + + yarn-cluster + Prepare info to apply the hbm + eu.dnetlib.dhp.oa.graph.hostedbymap.SparkPrepareHostedByInfoToApply + 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} + + --hostedByMapPath${hostedByMapPath} + --preparedInfoPath${workingDir}/preparedInfo + --graphPath${sourcePath} + --masteryarn-cluster + + + + + + + + + + + + + yarn-cluster + Apply hbm to result + eu.dnetlib.dhp.oa.graph.hostedbymap.SparkApplyHostedByMapToResult + dhp-graph-mapper-${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=${sparkSqlWarehouseDir} + + --outputPath${outputPath}/publication + --preparedInfoPath${workingDir}/preparedInfo + --graphPath${sourcePath} + --masteryarn-cluster + + + + + + + + yarn-cluster + Apply hbm to datasource + eu.dnetlib.dhp.oa.graph.hostedbymap.SparkApplyHostedByMapToDatasource + 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} + + --outputPath${outputPath}/datasource + --preparedInfoPath${workingDir}/preparedInfo + --graphPath${sourcePath} + --masteryarn-cluster + + + + + + From eb8c3f85944c8b915d455270d9a3ec2e26047244 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:19:17 +0200 Subject: [PATCH 26/51] Hosted By Map - test modified because of the application of the new aggregator on datasources --- .../java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala index b78eb978bf..c48c3b35d3 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala @@ -98,7 +98,7 @@ class TestApply extends java.io.Serializable{ val dats_ds :Dataset[Datasource] = spark.read.textFile(dats).map(p => mapper.readValue(p, classOf[Datasource])) - val hbm_ds :Dataset[EntityInfo] = spark.read.textFile(hbm).map(p => mapper.readValue(p, classOf[EntityInfo])) + val hbm_ds :Dataset[EntityInfo] = Aggregators.datasourceToSingleId(spark.read.textFile(hbm).map(p => mapper.readValue(p, classOf[EntityInfo]))) assertEquals(10, dats_ds.count()) @@ -122,7 +122,7 @@ class TestApply extends java.io.Serializable{ }else{ assertTrue(pa.getOpenairecompatibility().getClassid.equals(pb.getOpenairecompatibility.getClassid)) - assertTrue(pa.getOpenairecompatibility().getClassname.equals(pb.getOpenairecompatibility.getClassid)) + assertTrue(pa.getOpenairecompatibility().getClassname.equals(pb.getOpenairecompatibility.getClassname)) } }) From c7b71647c63cab956cb183775752df7c2b9d9b02 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 4 Aug 2021 10:20:02 +0200 Subject: [PATCH 27/51] Hosted By Map - modification of the resource for testing the presence of only one entry per datasource id --- .../eu/dnetlib/dhp/oa/graph/hostedbymap/preparedInfo2.json | 1 + 1 file changed, 1 insertion(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/preparedInfo2.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/preparedInfo2.json index 6e1cce3b6e..64e2433edb 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/preparedInfo2.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/preparedInfo2.json @@ -1,2 +1,3 @@ {"id":"pubid","journal_id":"issn","name":"ds_name","openaccess":true,"hb_id":"10|doajarticles::0ab37b7620eb9a73ac95d3ca4320c97d"} +{"id":"pubid","journal_id":"issn","name":"ds_name","openaccess":true,"hb_id":"10|doajarticles::0ab37b7620eb9a73ac95d3ca4320c97d"} {"id":"pubid","journal_id":"issn","name":"ds_name","openaccess":true,"hb_id":"10|doajarticles::abbc9265bea9ff62776a1c39785af00c"} From 2efa5abda5e4cbebcc4061c0f3866fe431d3163e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Mon, 9 Aug 2021 12:28:36 +0200 Subject: [PATCH 28/51] refactoring --- .../eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml | 2 -- 1 file changed, 2 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml index 30e500da3c..71b20b356d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/oozie_app/workflow.xml @@ -123,8 +123,6 @@ - - From 9731a6144a4ed9df6a513b81cc5c390b9328971b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Tue, 10 Aug 2021 17:49:45 +0200 Subject: [PATCH 29/51] hostedbymap - in case the journal is open access the access may be changed also for the best access right in the result --- .../dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala | 1 + 1 file changed, 1 insertion(+) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala index 312513285c..4c3b98f3b4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala @@ -34,6 +34,7 @@ object SparkApplyHostedByMapToResult { if (ei.getOpenaccess) { inst.setAccessright(OafMapperUtils.accessRight(ModelConstants.ACCESS_RIGHT_OPEN, "Open Access", ModelConstants.DNET_ACCESS_MODES, ModelConstants.DNET_ACCESS_MODES)) inst.getAccessright.setOpenAccessRoute(OpenAccessRoute.hybrid) + p.setBestaccessright(OafMapperUtils.createBestAccessRights(p.getInstance())); } } From b688567db5238276a7826b7f3e3ccd9962f44f53 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 10:12:10 +0200 Subject: [PATCH 30/51] hostedbymap - modified part of test to check the bestaccessright changed --- .../eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala | 8 ++++++-- .../eu/dnetlib/dhp/oa/graph/hostedbymap/publication.json | 2 +- 2 files changed, 7 insertions(+), 3 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala index c48c3b35d3..a48e527020 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/hostedbymap/TestApply.scala @@ -55,13 +55,17 @@ class TestApply extends java.io.Serializable{ assertTrue(pa.getInstance().get(0).getAccessright.getClassid.equals("OPEN")) assertTrue(pa.getInstance().get(0).getAccessright.getClassname.equals("Open Access")) assertTrue(pa.getInstance().get(0).getAccessright.getOpenAccessRoute.equals(OpenAccessRoute.hybrid)) + assertTrue(pa.getBestaccessright.getClassid.equals("OPEN")) + assertTrue(pa.getBestaccessright.getClassname.equals("Open Access")) assertTrue(pb.getInstance().get(0).getHostedby.getKey.equals("10|openaire____::0b74b6a356bbf23c245f9ae9a748745c")) assertTrue(pb.getInstance().get(0).getHostedby.getValue.equals("Revistas de investigación Universidad Nacional Mayor de San Marcos")) - assertTrue(pb.getInstance().get(0).getAccessright.getClassname.equals("Open Access")) - assertTrue(pb.getInstance().get(0).getAccessright.getClassid.equals("OPEN")) + assertTrue(pb.getInstance().get(0).getAccessright.getClassname.equals("not available")) + assertTrue(pb.getInstance().get(0).getAccessright.getClassid.equals("UNKNOWN")) assertTrue(pb.getInstance().get(0).getAccessright.getOpenAccessRoute == null) + assertTrue(pb.getBestaccessright.getClassid.equals("UNKNOWN")) + assertTrue(pb.getBestaccessright.getClassname.equals("not available")) }else{ assertTrue(pa.getInstance().get(0).getHostedby.getKey.equals(pb.getInstance().get(0).getHostedby.getKey)) diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/publication.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/publication.json index 602bedbdad..8f6842bf35 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/publication.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/hostedbymap/publication.json @@ -7,7 +7,7 @@ {"author":[{"fullname":"López-Lambas, M.","name":"M.","pid":[],"rank":1,"surname":"López-Lambas"},{"fullname":"López-Suárez, E.","name":"E.","pid":[],"rank":2,"surname":"López-Suárez"},{"fullname":"La Paix-Puello, L.","name":"L.","pid":[],"rank":3,"surname":"La Paix-Puello"},{"fullname":"Binsted, A.","name":"A.","pid":[],"rank":4,"surname":"Binsted"},{"fullname":"Tuominen, Anu","name":"Anu","pid":[],"rank":5,"surname":"Tuominen"},{"fullname":"Järvi, Tuuli","name":"Tuuli","pid":[],"rank":6,"surname":"Järvi"}],"bestaccessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT Research Information System"}],"context":[],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2009-01-01"},"dateofcollection":"2021-07-10T12:26:56.401Z","dateoftransformation":"2021-07-10T14:03:19.178Z","description":[],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|355e65625b88::899c4bc19c11e4e4ebe8d49a8c51c5f4","instance":[{"accessright":{"classid":"RESTRICTED","classname":"Restricted","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::4692342f0992d91f9e705c26959f09e0","value":"VTT 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An automatic gamma spectrometer for activation analysis has been developed at the Technical Research Centre of Finland. The on-line system comprises a sample changer for up to 120 samples, detector, multichannel analyzer, microcomputer programmed with Basic language and input/output devices.

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To carry out this diagnosis the instrument of the Iberoamerican University Association was taken into account. The following variables were used: students, teachers, study plans, research, management, surroundings, graduates and impact and evaluation. According to the established measurement the post graduate unit has obtained 69,27 points, which places it on a good level. This level considers a range point from 60 through 74."},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"La investigación realiza un diagnóstico de la Unidad de Post Grado de la Facultad de Educación de la UNMSM, con la participación de 358 estudiantes de Segunda Especialidad, Maestrías y Doctorado. 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Realizado el diagnóstico de acuerdo a la medición establecida la UPG de Educación de acuerdo al puntaje obtenido de 69, 27 se ubica en el nivel bueno, ya que dicho nivel considera las puntuaciones comprendidas entre 60 y 74."}],"externalReference":[],"extraInfo":[],"format":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"application/pdf"}],"fulltext":[],"id":"50|4dc99724cf04::ed1ba83e1add6ce292433729acd8b0d9","instance":[{"accessright":{"classid":"UNKNOWN","classname":"not available","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::0b74b6a356bbf23c245f9ae9a748745c","value":"Revistas de investigación Universidad Nacional Mayor de San Marcos"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2014-06-30"},"distributionlocation":"","hostedby":{"key":"10|openaire____::0b74b6a356bbf23c245f9ae9a748745c","value":"Revistas de investigación Universidad Nacional Mayor de San Marcos"},"instancetype":{"classid":"0001","classname":"Article","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"license":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"http://creativecommons.org/licenses/by-nc-sa/4.0"},"pid":[],"refereed":{"classid":"0000","classname":"Unknown","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["https://revistasinvestigacion.unmsm.edu.pe/index.php/educa/article/view/4754"]}],"journal":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"edition":"","ep":"","iss":"","issnLinking":"","issnOnline":"0001-396X","issnPrinted":"1728-5852","name":"Investigación Educativa","sp":"","vol":""},"language":{"classid":"spa","classname":"Spanish; Castilian","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1627812364983,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"https%3A%2F%2Frevistasinvestigacion.unmsm.edu.pe%2Findex.php%2Findex%2Foai","datestamp":"2021-03-06T03:56:00Z","harvestDate":"2021-03-12T07:05:02.842Z","identifier":"oai:ojs.csi.unmsm:article/4754","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"originalId":["50|4dc99724cf04::ed1ba83e1add6ce292433729acd8b0d9","oai:ojs.csi.unmsm:article/4754"],"pid":[],"publisher":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Facultad de Educación, Universidad Nacional Mayor de San Marcos"},"relevantdate":[],"resourcetype":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Investigación Educativa; Vol 14 No 25 (2010); 29 - 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U ovom je radu odabirom pet ekoloških indikatora obuhvaćena ekološka komponenta. Indikatori su birani s obzirom na učestalost njihova predlaganja i korištenja u dokumentima Europske unije (EU) i znanstvenim radovima. Cilj rada je vrednovati ekološke indikatore uz argumentiranje njihove važnosti za postizanje održivog ruralnog razvoja provođenjem ankete među ekspertima i različitim dionicima ruralnog razvoja. U anketi je sudjelovalo 47 ispitanika. 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CROSBI"}],"context":[],"contributor":[],"country":[],"coverage":[],"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2014-01-01"},"dateofcollection":"2021-07-11T01:23:38.842Z","dateoftransformation":"2021-07-11T02:01:53.063Z","description":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"Die Filme Michael Hanekes scheinen vor allem mit jenen des späten Pasolini zu korrespondieren, allen voran mit SALÒ aber auch mit TEOREMA, jenem Film, in dem sich Pasolini dem italienischen Großbürgertum der ausgehenden 1960er Jahre widmet. Erzählt wird in TEOREMA die Geschichte einer zu Beginn des Films anscheinend intakten Familie, die sich durch die Begegnung mit einem Unbekannten der eigenen Leere bewusst wird und auseinanderfällt. Der Film endet mit dem Schrei eines der Protagonisten, der hier jedoch weniger ein neues Leben bedeutet, als vielmehr eine Reaktion auf die repressiven und normativen Mechanismen der Gesellschaft. Hanekes Filme LEMMINGE, TEIL II und DER SIEBENTE KONTINENT gehen jeweils unter-schiedlich von einer vergleichbaren Prämisse einer leeren Familie aus. Doch während die Schreie in den LEMMINGEN immer lauter werden, verstummen sie im SIEBENTEN KONTINENT schließlich. In allen benannten Filmen hat das Werk Francis Bacons eine besondere Rolle gespielt und wurde entweder explizit (TEOREMA, LEMMINGE II) oder implizit (DER SIEBENTE KONTINENT) thematisiert. Der Vortrag geht den Bildern des (stummen) Schreis in den genannten Filmen nach."}],"externalReference":[],"extraInfo":[],"format":[],"fulltext":[],"id":"50|57a035e5b1ae::023bc0883fb1075fe0a86e829b6c5d97","instance":[{"accessright":{"classid":"CLOSED","classname":"Closed Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"alternateIdentifier":[],"collectedfrom":{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"},"dateofacceptance":{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"value":"2014-01-01"},"hostedby":{"key":"10|openaire____::345c9d171ef3c5d706d08041d506428c","value":"Croatian Scientific Bibliography - CROSBI"},"instancetype":{"classid":"0004","classname":"Conference object","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"pid":[],"refereed":{"classid":"0000","classname":"Unknown","schemeid":"dnet:review_levels","schemename":"dnet:review_levels"},"url":["https://www.bib.irb.hr/848053"]}],"language":{"classid":"deu/ger","classname":"German","schemeid":"dnet:languages","schemename":"dnet:languages"},"lastupdatetimestamp":1627813203778,"oaiprovenance":{"originDescription":{"altered":true,"baseURL":"https%3A%2F%2Fbib.irb.hr%2Foai2%2F","datestamp":"2016-12-06T18:47:39Z","harvestDate":"2021-07-11T01:23:38.842Z","identifier":"848053","metadataNamespace":""}},"originalId":["848053","50|57a035e5b1ae::023bc0883fb1075fe0a86e829b6c5d97"],"pid":[],"relevantdate":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.9"},"qualifier":{"classid":"issued","classname":"issued","schemeid":"dnet:dataCite_date","schemename":"dnet:dataCite_date"},"value":"2014-01-01"}],"resourcetype":{"classid":"UNKNOWN","classname":"Unknown","schemeid":"dnet:dataCite_resource","schemename":"dnet:dataCite_resource"},"resulttype":{"classid":"publication","classname":"publication","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"source":[],"subject":[],"title":[{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","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":"\"Teorema\" von Pier Paolo Pasolini oder: Ein Schrei auf Francis Bacons Spuren"},{"dataInfo":{"deletedbyinference":false,"inferenceprovenance":"","inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:datasetarchive","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":"\"Teorema\" by Pier Paolo Pasolini"}]} \ No newline at end of file From 52c18c2697b17e17916284b7b2f028ad28df7bcf Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 16:16:55 +0200 Subject: [PATCH 31/51] removed not needed test class. Teh functionality has been moved --- .../eu/dnetlib/dhp/doiboost/GetCSVTest.java | 43 ------------------- 1 file changed, 43 deletions(-) delete mode 100644 dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/GetCSVTest.java diff --git a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/GetCSVTest.java b/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/GetCSVTest.java deleted file mode 100644 index 6cfc90736e..0000000000 --- a/dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/dhp/doiboost/GetCSVTest.java +++ /dev/null @@ -1,43 +0,0 @@ - -package eu.dnetlib.dhp.doiboost; - -import java.util.List; - -import org.apache.commons.io.IOUtils; -import org.junit.jupiter.api.Assertions; -import org.junit.jupiter.api.Test; - -import com.fasterxml.jackson.core.JsonProcessingException; -import com.fasterxml.jackson.databind.ObjectMapper; - -import eu.dnetlib.dhp.actionmanager.project.utils.CSVParser; - -public class GetCSVTest { - - @Test - public void readUnibiGoldTest() throws Exception { - - String programmecsv = IOUtils - .toString( - getClass() - .getClassLoader() - .getResourceAsStream("eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv")); - - CSVParser csvParser = new CSVParser(); - - List pl = csvParser.parse(programmecsv, "eu.dnetlib.doiboost.UnibiGoldModel", ','); - - Assertions.assertEquals(72, pl.size()); - -// ObjectMapper OBJECT_MAPPER = new ObjectMapper(); -// -// pl.forEach(res -> { -// try { -// System.out.println(OBJECT_MAPPER.writeValueAsString(res)); -// } catch (JsonProcessingException e) { -// e.printStackTrace(); -// } -// }); - - } -} From b1c6140ebf01608af7792d4d528c83ea62760616 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 16:23:33 +0200 Subject: [PATCH 32/51] removed all comments in Italian --- .../hostedbymap/SparkApplyHostedByMapToDatasource.scala | 2 -- .../hostedbymap/SparkApplyHostedByMapToResult.scala | 5 ----- .../hostedbymap/SparkPrepareHostedByInfoToApply.scala | 9 +++++---- 3 files changed, 5 insertions(+), 11 deletions(-) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala index fad313f1cd..ae1454b479 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToDatasource.scala @@ -61,8 +61,6 @@ object SparkApplyHostedByMapToDatasource { val pinfo : Dataset[EntityInfo] = Aggregators.datasourceToSingleId( spark.read.textFile(preparedInfoPath) .map(ei => mapper.readValue(ei, classOf[EntityInfo]))) - //c. dataset join risultato del passo prima di a per datasource id, gruppo per ds id e cambio compatibilita' se necessario - applyHBtoDats(pinfo, dats).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/hostedbymap/SparkApplyHostedByMapToResult.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala index 4c3b98f3b4..533e439b7f 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkApplyHostedByMapToResult.scala @@ -14,9 +14,6 @@ import org.slf4j.{Logger, LoggerFactory} import scala.collection.JavaConverters._ -//a. publication join risultato del passo precedente su result id (left) setto la istanza (se piu' di una instance -// nel result => salto)con l'hosted by anche access right della instance se openaccess e' true - object SparkApplyHostedByMapToResult { @@ -76,8 +73,6 @@ object SparkApplyHostedByMapToResult { val pinfo : Dataset[EntityInfo] = spark.read.textFile(preparedInfoPath) .map(ei => mapper.readValue(ei, classOf[EntityInfo])) - //a. publication join risultato del passo precedente su result id (left) setto la istanza (se piu' di una instance - // nel result => salto)con l'hosted by anche access right della instance se openaccess e' true applyHBtoPubs(pinfo, pubs).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/hostedbymap/SparkPrepareHostedByInfoToApply.scala b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala index d342d57b07..6db0ad33db 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/hostedbymap/SparkPrepareHostedByInfoToApply.scala @@ -106,14 +106,15 @@ object SparkPrepareHostedByInfoToApply { import spark.implicits._ - //STEP1: leggere la hostedbymap e trasformarla in entity info + //STEP1: read the hostedbymap and transform it in EntityInfo val hostedByInfo:Dataset[EntityInfo] = spark.createDataset(spark.sparkContext.textFile(hostedByMapPath)).map(toEntityInfo) - //STEP2: creare la mappa publication id issn, eissn, lissn esplosa + //STEP2: create association (publication, issn), (publication, eissn), (publication, lissn) val resultInfoDataset:Dataset[EntityInfo] = prepareResultInfo(spark, graphPath + "/publication") - //STEP3: join resultInfo con hostedByInfo sul journal_id dal result con left - // e riduzione di tutti i result con lo stesso id in una unica entry con aggiunto l'id della datasource + //STEP3: left join resultInfo with hostedByInfo on journal_id. Reduction of all the results with the same id in just + //one entry (one result could be associated to issn and eissn and so possivly matching more than once against the map) + //to this entry we add the id of the datasource for the next step joinResHBM(resultInfoDataset, hostedByInfo) .write.mode(SaveMode.Overwrite).option("compression", "gzip").json(outputPath) From 822963283954830d16429411e983529de815b179 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 16:36:01 +0200 Subject: [PATCH 33/51] adding assertions to the mapping of the unibi part of gold list --- .../dhp/oa/graph/hostedbymap/TestReadCSV.java | 18 ++++++++---------- 1 file changed, 8 insertions(+), 10 deletions(-) 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 index f886b275b4..98b811bb65 100644 --- 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 @@ -7,6 +7,8 @@ import java.net.URLConnection; import java.nio.charset.Charset; import java.util.List; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.Disabled; import org.junit.jupiter.api.Test; import com.fasterxml.jackson.core.JsonProcessingException; @@ -29,18 +31,13 @@ public class TestReadCSV { .build() .parse(); - ObjectMapper mapper = new ObjectMapper(); - - beans.forEach(r -> { - try { - System.out.println(mapper.writeValueAsString(r)); - } catch (JsonProcessingException e) { - e.printStackTrace(); - } - }); + Assertions.assertEquals(36, beans.size()); + Assertions.assertEquals(1, beans.stream().filter(e -> e.getIssn().equals("0001-625X")).count()); + Assertions.assertTrue(beans.stream().anyMatch(e -> e.getIssn().equals("0001-625X") && e.getTitle().equals("Acta Mycologica"))); + Assertions.assertTrue(beans.stream().allMatch(e -> e.getIssn().equals(e.getIssn_l()))); } - + @Disabled @Test public void testCSVUrlUnibi() throws IOException { @@ -66,6 +63,7 @@ public class TestReadCSV { ); } + @Disabled @Test public void testCSVUrlDOAJ() throws IOException { From f9b6b45d85e3ea9e676062366a2e249de1f7bd03 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:04:48 +0200 Subject: [PATCH 34/51] reverting --- .../src/test/resources/eu/dnetlib/dhp/transform/terms.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 30138b5bcf..93cc00eca4 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 From 55fc500d8d0d6736ca10e06c01e83c784299e93f Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:17:48 +0200 Subject: [PATCH 35/51] reverting --- .../src/test/resources/eu/dnetlib/dhp/transform/input_itgv4.xml | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 b421f1342a..06325810b4 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 From 7aa3260729a7a145842958526d3feedfa3461e8c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:18:45 +0200 Subject: [PATCH 36/51] reverting --- .../original/dc_cleaning_OPENAIREplus_compliant_hal_orig | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) 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 505f562941..d4eb71dc42 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";); From 524c06e0283244758df98add2d622db44dd7f16b Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:20:30 +0200 Subject: [PATCH 37/51] reverting --- ...e_datacite_ExchangeLandingpagePid_orig.xsl | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) 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 f80c91a6a2..3cfaec80b1 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 @@ - + - + From 804589eb30f616314c9d9e01c0681312548e2777 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:23:35 +0200 Subject: [PATCH 39/51] reverting --- .../src/test/resources/eu/dnetlib/dhp/transform/terms.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 30138b5bcf..93cc00eca4 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 From b6b58bba281176ea534c75cee5a440b99ac4908c Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:25:37 +0200 Subject: [PATCH 40/51] reverting --- .../eu.dnetlib.dhp.doiboost.mappings/crossref_mapping.csv | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 0c1fd9e64b..6a5fc3f871 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, From c6a2a780a9b181395ae455a661ff620ecbcb6f22 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:30:17 +0200 Subject: [PATCH 41/51] reverting --- .../src/test/resources/eu/dnetlib/dhp/oa/graph/clean/terms.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 4db5fd463d..ba47aaf5c8 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 From 0e1a6bec20edf4995f9ccb9825907f3a545f3817 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:32:29 +0200 Subject: [PATCH 42/51] reverting --- .../resources/eu/dnetlib/dhp/oa/graph/raw/oaf_claim_dedup.xml | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) 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 b45fa1edba..95457fb701 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 From 8ad7c7141702b3a1638d7d1abe26889f300ea480 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:36:12 +0200 Subject: [PATCH 43/51] reverting --- .../dhp/sx/graph/bio/pubmed/pubmed.xml | 46 +++++++++---------- 1 file changed, 23 insertions(+), 23 deletions(-) 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 06ebe97cd5..22da07e299 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 From b9663298330212499fef14413b35ced9d336dc57 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:37:00 +0200 Subject: [PATCH 44/51] reverting --- .../src/test/resources/eu/dnetlib/dhp/transform/terms.txt | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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 30138b5bcf..93cc00eca4 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 From cc3d72df0e9dd8781e0ae8ae59b57032bca4098e Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:42:01 +0200 Subject: [PATCH 45/51] removing not needed dependency --- dhp-common/pom.xml | 6 +----- 1 file changed, 1 insertion(+), 5 deletions(-) diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index a6a57ce7b1..c66c1d3bc4 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -118,11 +118,7 @@ dhp-schemas - - org.apache.commons - commons-csv - 1.8 - + From 95e5482bbb35acc1ae269fb018017ec3f8240583 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:42:26 +0200 Subject: [PATCH 46/51] removing not needed dependency --- dhp-workflows/dhp-doiboost/pom.xml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index ea8832754d..385f87ad2f 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -82,12 +82,6 @@ org.apache.commons commons-text - - eu.dnetlib.dhp - dhp-aggregation - 1.2.4-SNAPSHOT - compile - From 785db1d5b2c26cf3e81bc9a38b54ec60c26764f9 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:44:07 +0200 Subject: [PATCH 47/51] refactoring --- .../eu/dnetlib/dhp/oa/graph/hostedbymap/TestReadCSV.java | 7 ++++++- 1 file changed, 6 insertions(+), 1 deletion(-) 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 index 98b811bb65..89259d8147 100644 --- 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 @@ -33,10 +33,15 @@ public class TestReadCSV { Assertions.assertEquals(36, beans.size()); Assertions.assertEquals(1, beans.stream().filter(e -> e.getIssn().equals("0001-625X")).count()); - Assertions.assertTrue(beans.stream().anyMatch(e -> e.getIssn().equals("0001-625X") && e.getTitle().equals("Acta Mycologica"))); + Assertions + .assertTrue( + beans + .stream() + .anyMatch(e -> e.getIssn().equals("0001-625X") && e.getTitle().equals("Acta Mycologica"))); Assertions.assertTrue(beans.stream().allMatch(e -> e.getIssn().equals(e.getIssn_l()))); } + @Disabled @Test public void testCSVUrlUnibi() throws IOException { From 9650eea497b3d131fab34f37afab12c872a26afc Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:45:48 +0200 Subject: [PATCH 48/51] reverting --- dhp-common/pom.xml | 6 ------ 1 file changed, 6 deletions(-) diff --git a/dhp-common/pom.xml b/dhp-common/pom.xml index c66c1d3bc4..4c7810c47c 100644 --- a/dhp-common/pom.xml +++ b/dhp-common/pom.xml @@ -117,12 +117,6 @@ eu.dnetlib.dhp dhp-schemas - - - - - - From e33daaeee89b253cde8968a8c33cad4b346e9aae Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:46:19 +0200 Subject: [PATCH 49/51] reverting --- dhp-workflows/dhp-doiboost/pom.xml | 1 + 1 file changed, 1 insertion(+) diff --git a/dhp-workflows/dhp-doiboost/pom.xml b/dhp-workflows/dhp-doiboost/pom.xml index 385f87ad2f..f496ea9a29 100644 --- a/dhp-workflows/dhp-doiboost/pom.xml +++ b/dhp-workflows/dhp-doiboost/pom.xml @@ -84,6 +84,7 @@ + From ac417ca798b07e77765d12ffe8c3c3774b1bc111 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 17:50:33 +0200 Subject: [PATCH 50/51] removed not needed test resource --- .../dhp/doiboost/issn_gold_oa_version_4.csv | 73 ------------------- 1 file changed, 73 deletions(-) delete mode 100644 dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv 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 deleted file mode 100644 index ebde1bf189..0000000000 --- a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/dhp/doiboost/issn_gold_oa_version_4.csv +++ /dev/null @@ -1,73 +0,0 @@ -"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" -"0003-424X","0003-424X",0,1,0,0,1,0,0,1,0,0,1,0,"Annales de zootechnie.","ROAD" -"0003-4827","0003-4827",0,1,0,0,0,1,0,1,0,0,0,1,"Annals of Iowa.","ROAD" -"0004-0592","0004-0592",1,1,0,0,1,1,1,1,0,0,1,1,"Archivos de Zootecnia","DOAJ" -"0004-282X","0004-282X",1,1,0,0,1,1,1,1,0,0,1,1,"Arquivos de Neuro-Psiquiatria","DOAJ" -"0006-3096","0006-3096",0,1,0,0,0,0,0,1,0,0,0,0,"Biologia.","ROAD" -"0006-8705","0006-8705",1,1,0,0,1,1,1,1,0,0,1,1,"Bragantia","DOAJ" -"0007-5124","0007-5124",0,1,0,0,1,0,0,1,1,0,1,1,"Experimental animals.","ROAD" -"0007-9502","0007-9502",0,1,0,0,0,0,0,1,0,0,0,0,"Caesaraugusta.","ROAD" -"0008-7386","0008-7386",1,1,0,0,0,1,1,1,0,0,0,1,"Časopis pro Moderní Filologii","DOAJ" -"0008-7629","0008-7629",1,0,0,0,0,0,1,0,0,0,0,0,"Catalogue and Index","DOAJ" -"0015-573X","0015-573X",0,1,0,0,0,0,0,1,0,0,0,0,"Folia quaternaria.","ROAD" -"0016-6987","0016-6987",1,0,0,0,1,1,1,0,0,0,1,1,"Genus","DOAJ" -"0016-7789","0016-7789",1,1,0,0,0,1,1,1,0,0,0,1,"Geologija ","DOAJ" -"0021-5007","0021-5007",0,1,0,0,0,1,0,1,0,0,0,1,"Nihon Seitai Gakkaishi.","ROAD" -"0023-4001","0023-4001",0,1,0,0,1,1,0,1,0,0,1,1,"Korean Journal of Parasitology","ROAD" -"0023-5415","0023-5415",1,1,0,0,0,0,1,1,0,0,0,0,"Kunst og Kultur","DOAJ" -"0026-1165","0026-1165",1,0,0,0,1,1,1,0,0,0,1,1,"Journal of the Meteorological Society of Japan","DOAJ" -"0029-0181","0029-0181",0,1,0,0,0,0,0,1,0,0,0,0,"Nihon butsuri gakkaishi.","ROAD" -"0034-7000","0034-7000",1,1,0,0,0,1,1,1,0,0,0,1,"Revista Argentina de Cardiología","DOAJ" -"0034-7523","0034-7523",0,1,0,0,0,1,0,1,0,0,0,1,"Revista cubana de medicina.","ROAD" -"0034-8244","0034-8244",1,0,0,0,1,1,1,0,0,0,1,1,"Revista de Filosofia","DOAJ" -"0034-8678","0034-8678",1,0,0,0,0,0,1,0,0,0,0,0,"Revista de Pedagogie","DOAJ" -"0036-8709","0036-8709",1,1,1,0,1,1,1,1,1,0,1,1,"Scientia Pharmaceutica","DOAJ" -"0044-4855","0044-4855",0,1,0,0,0,0,0,1,0,0,0,0,"Život i škola.","ROAD" -"0048-7449","0048-7449",1,1,0,0,1,1,1,1,0,0,1,1,"Reumatismo","DOAJ" -"0048-766X","0048-766X",0,1,0,0,0,1,0,1,0,0,0,1,"Revista chilena de obstetricia y ginecología.","ROAD" -"0065-1400","0065-1400",0,1,0,0,1,1,0,1,0,0,1,1,"Acta Neurobiologiae Experimentalis.","ROAD" -"0066-6742","0066-6742",1,0,0,0,1,1,1,0,0,0,1,1,"Archivo Español de Arqueología","DOAJ" -"0073-2435","0073-2435",1,1,0,0,1,1,1,1,0,0,1,1,"Historia (Santiago)","DOAJ" -"0073-4918","0073-4918",0,1,0,0,0,0,0,1,0,0,0,0,"Illinois Natural History Survey bulletin.","ROAD" -"0075-7411","0075-7411",1,0,0,0,0,0,1,0,0,0,0,0,"Anales","DOAJ" -"0077-2704","0077-2704",0,1,0,0,0,0,0,1,0,0,0,0,"Namn och bygd.","ROAD" -"0078-5466","0078-5466",0,1,0,0,1,1,0,1,0,0,1,1,"Optica Applicata.","ROAD" -"0079-4929","0079-4929",1,1,0,0,0,0,1,1,0,0,0,0,"Právněhistorické studie","DOAJ" -"0100-3283","0100-3283",0,1,0,0,0,0,0,1,0,0,0,0,"Hansenologia Internationalis.","ROAD" -"0100-4042","0100-4042",1,1,0,0,1,1,1,1,0,0,1,1,"Química Nova","DOAJ" -"0100-8692","0100-8692",1,1,0,0,1,0,1,1,0,0,1,1,"Arquivos Brasileiros de Psicologia ","DOAJ" -"0102-4469","0102-4469",1,0,0,0,0,0,1,0,0,0,0,0,"Perspectiva Teológica","DOAJ" -"0102-6992","0102-6992",1,1,0,0,0,1,1,1,0,0,0,1,"Sociedade e Estado","DOAJ" -"0103-1570","0103-1570",1,1,0,0,0,0,1,1,0,0,0,0,"Revista Sociedade & Natureza","DOAJ" -"0103-2070","0103-2070",1,1,0,0,1,1,1,1,0,0,1,1,"Tempo Social","DOAJ" -"0104-0588","0104-0588",1,1,0,0,1,0,1,1,0,0,1,0,"Revista de Estudos da Linguagem","DOAJ" -"0104-6497","0104-6497",1,1,0,0,1,0,1,1,0,0,1,0,"Nauplius","DOAJ" -"0104-8929","0104-8929",0,1,0,0,0,0,0,1,0,0,0,0,"Saeculum.","ROAD" -"0104-9496","0104-9496",1,0,0,0,0,0,1,0,0,0,0,0,"Revista do Direito","DOAJ" -"0120-0380","0120-0380",0,1,0,0,1,0,0,1,0,0,1,0,"Boletín de matemáticas.","ROAD" -"0120-100X","0120-100X",1,1,0,0,0,0,1,1,0,0,0,0,"Revista Ion","DOAJ" -"0120-4807","0120-4807",1,1,0,0,0,0,1,1,0,0,0,0,"Universitas Humanística","DOAJ" -"0121-4004","0121-4004",1,0,0,0,1,1,1,0,0,0,1,1,"Vitae","DOAJ" -"0121-4500","0121-4500",1,1,0,0,0,0,1,1,0,0,0,0,"Avances en Enfermería","DOAJ" -"0121-8697","0121-8697",1,0,0,0,0,0,1,0,0,0,0,0,"Revista de Derecho","DOAJ" -"0122-5197","0122-5197",0,1,0,0,0,1,0,1,0,0,0,1,"Memoria y Sociedad.","ROAD" -"0161-0457","0161-0457",1,0,1,1,1,1,1,0,1,1,1,1,"Scanning","DOAJ" -"0215-4706","0215-4706",1,1,0,0,0,0,1,1,0,0,0,0,"Floribunda.","ROAD" -"0324-6000","0324-6000",0,1,0,0,1,1,0,1,0,0,1,1,"Periodica polytechnica. Electrical engineering","ROAD" -"0325-187X","0325-187X",1,1,0,0,0,1,1,1,0,0,0,1,"Meteorologica","DOAJ" -"0326-7237","0326-7237",1,1,0,0,0,1,1,1,0,0,0,1,"Geoacta.","ROAD" -"0327-1676","0327-1676",0,1,0,0,0,0,1,1,0,0,0,0,"Andes","DOAJ" -"0327-2818","0327-2818",1,0,0,0,0,0,1,0,0,0,0,0,"Dominguezia","DOAJ" -"0327-5108","0327-5108",1,0,0,0,0,0,1,0,0,0,0,0,"Páginas de Filosofía","DOAJ" -"0327-585X","0327-585X",1,1,0,0,0,0,1,1,0,0,0,0,"Actualidad Económica","DOAJ" -"0327-6147","0327-6147",0,1,0,0,0,0,0,1,0,0,0,0,"Papeles de trabajo.","ROAD" -"0327-7763","0327-7763",0,1,0,0,0,0,0,1,0,0,0,0,"Revista del IICE.","ROAD" -"0327-9286","0327-9286",1,1,0,0,0,0,1,1,0,0,0,0,"Acta Toxicológica Argentina","DOAJ" -"0328-1205","0328-1205",1,1,0,0,1,1,1,1,0,0,1,1,"Synthesis (La Plata)","DOAJ" -"0329-5893","0329-5893",0,1,0,0,0,0,0,1,0,0,0,0,"Investigaciones en psicología..","ROAD" -"0329-8213","0329-8213",1,0,0,0,0,0,1,0,0,0,0,0,"Historia Regional","DOAJ" -"0332-5024","0332-5024",1,1,0,0,0,0,1,1,0,0,0,0,"Studia Musicologica Norvegica","DOAJ" -"0350-185X","0350-185X",1,1,0,0,0,0,1,1,0,0,0,0,"Južnoslovenski Filolog","DOAJ" From 08dd2b2102c3a8074c854839cc4b18f948d24b95 Mon Sep 17 00:00:00 2001 From: "miriam.baglioni" Date: Wed, 11 Aug 2021 18:09:41 +0200 Subject: [PATCH 51/51] moving the dependency version to the external pom file --- dhp-workflows/dhp-graph-mapper/pom.xml | 1 - pom.xml | 6 ++++++ 2 files changed, 6 insertions(+), 1 deletion(-) diff --git a/dhp-workflows/dhp-graph-mapper/pom.xml b/dhp-workflows/dhp-graph-mapper/pom.xml index 665c01276a..6c5e4609a3 100644 --- a/dhp-workflows/dhp-graph-mapper/pom.xml +++ b/dhp-workflows/dhp-graph-mapper/pom.xml @@ -125,7 +125,6 @@ com.opencsv opencsv - 5.5 diff --git a/pom.xml b/pom.xml index 433c880930..d31ffb88d5 100644 --- a/pom.xml +++ b/pom.xml @@ -519,6 +519,12 @@ ${common.text.version} + + com.opencsv + opencsv + 5.5 + +