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[eosc_services] resolved merge conflicts

This commit is contained in:
Claudio Atzori 2022-05-03 13:37:15 +02:00
parent 78015a5733 9e12cb3c92
commit da611cfbbd
19 changed files with 1058 additions and 317 deletions
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13
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java
View File

@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.oaf.utils;
import static eu.dnetlib.dhp.schema.common.ModelConstants.*; import static eu.dnetlib.dhp.schema.common.ModelConstants.*;
import java.sql.Array;
import java.sql.SQLException;
import java.util.*; import java.util.*;
import java.util.concurrent.ConcurrentHashMap; import java.util.concurrent.ConcurrentHashMap;
import java.util.function.Function; import java.util.function.Function;
@ -118,6 +120,17 @@ public class OafMapperUtils {
.collect(Collectors.toList()); .collect(Collectors.toList());
} }
public static <T> List<T> listValues(Array values) throws SQLException {
if (Objects.isNull(values)) {
return null;
}
return Arrays
.stream((T[]) values.getArray())
.filter(Objects::nonNull)
.distinct()
.collect(Collectors.toList());
}
public static List<Field<String>> listFields(final DataInfo info, final List<String> values) { public static List<Field<String>> listFields(final DataInfo info, final List<String> values) {
return values return values
.stream() .stream()

185
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java
View File

@ -44,105 +44,104 @@ class OafMapperUtilsTest {
@Test @Test
void testDateValidation() { void testDateValidation() {
assertTrue(GraphCleaningFunctions.doCleanDate("2016-05-07T12:41:19.202Z ").isPresent()); assertNotNull(GraphCleaningFunctions.cleanDate("2016-05-07T12:41:19.202Z "));
assertTrue(GraphCleaningFunctions.doCleanDate("2020-09-10 11:08:52 ").isPresent()); assertNotNull(GraphCleaningFunctions.cleanDate("2020-09-10 11:08:52 "));
assertTrue(GraphCleaningFunctions.doCleanDate(" 2016-04-05").isPresent()); assertNotNull(GraphCleaningFunctions.cleanDate(" 2016-04-05"));
assertEquals("2016-04-05", GraphCleaningFunctions.doCleanDate("2016 Apr 05").get()); assertEquals("2016-04-05", GraphCleaningFunctions.cleanDate("2016 Apr 05"));
assertEquals("2009-05-08", GraphCleaningFunctions.doCleanDate("May 8, 2009 5:57:51 PM").get()); assertEquals("2009-05-08", GraphCleaningFunctions.cleanDate("May 8, 2009 5:57:51 PM"));
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, 1970").get()); assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, 1970"));
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, '70").get()); assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, '70"));
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 1970").get()); assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 1970"));
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 70").get()); assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 70"));
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 2006").get()); assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 2006"));
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 MST 2006").get()); assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 MST 2006"));
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 02 15:04:05 -0700 2006").get()); assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 02 15:04:05 -0700 2006"));
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Monday, 02-Jan-06 15:04:05 MST").get()); assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Monday, 02-Jan-06 15:04:05 MST"));
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 MST").get()); assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 MST"));
assertEquals("2017-07-11", GraphCleaningFunctions.doCleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)").get()); assertEquals("2017-07-11", GraphCleaningFunctions.cleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)"));
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 -0700").get()); assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 -0700"));
assertEquals("2018-01-04", GraphCleaningFunctions.doCleanDate("Thu, 4 Jan 2018 17:53:36 +0000").get()); assertEquals("2018-01-04", GraphCleaningFunctions.cleanDate("Thu, 4 Jan 2018 17:53:36 +0000"));
assertEquals("2015-08-10", GraphCleaningFunctions.doCleanDate("Mon Aug 10 15:44:11 UTC+0100 2015").get()); assertEquals("2015-08-10", GraphCleaningFunctions.cleanDate("Mon Aug 10 15:44:11 UTC+0100 2015"));
assertEquals( assertEquals(
"2015-07-03", "2015-07-03",
GraphCleaningFunctions.doCleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)").get()); GraphCleaningFunctions.cleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)"));
assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 10:09am").get()); assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 10:09am"));
assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 at 10:09am PST-08").get()); assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 at 10:09am PST-08"));
assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012, 10:10:09").get()); assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012, 10:10:09"));
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7, 1970").get()); assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7, 1970"));
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7th, 1970").get()); assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7th, 1970"));
assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006, 19:17").get()); assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006, 19:17"));
assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006 19:17").get()); assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006 19:17"));
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 70").get()); assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 70"));
assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 1970").get()); assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 1970"));
assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("03 February 2013").get()); assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("03 February 2013"));
assertEquals("2013-07-01", GraphCleaningFunctions.doCleanDate("1 July 2013").get()); assertEquals("2013-07-01", GraphCleaningFunctions.cleanDate("1 July 2013"));
assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("2013-Feb-03").get()); assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("2013-Feb-03"));
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3/31/2014").get()); assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3/31/2014"));
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03/31/2014").get()); assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03/31/2014"));
assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08/21/71").get()); assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08/21/71"));
assertEquals("1971-01-08", GraphCleaningFunctions.doCleanDate("8/1/71").get()); assertEquals("1971-01-08", GraphCleaningFunctions.cleanDate("8/1/71"));
assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/2014 22:05").get()); assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/2014 22:05"));
assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("04/08/2014 22:05").get()); assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("04/08/2014 22:05"));
assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/14 22:05").get()); assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/14 22:05"));
assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("04/2/2014 03:00:51").get()); assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("04/2/2014 03:00:51"));
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00:00 AM").get()); assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00:00 AM"));
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00:01 PM").get()); assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00:01 PM"));
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00 PM").get()); assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00 PM"));
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 1:00 PM").get()); assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 1:00 PM"));
assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00 AM").get()); assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00 AM"));
assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("4/02/2014 03:00:51").get()); assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("4/02/2014 03:00:51"));
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59").get()); assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59"));
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59.3186369").get()); assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59.3186369"));
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/3/31").get()); assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/3/31"));
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/03/31").get()); assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/03/31"));
assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/4/8 22:05").get()); assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/4/8 22:05"));
assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/04/08 22:05").get()); assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/04/08 22:05"));
assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/04/2 03:00:51").get()); assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/04/2 03:00:51"));
assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/4/02 03:00:51").get()); assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/4/02 03:00:51"));
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59").get()); assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59"));
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59.3186369").get()); assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59.3186369"));
assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014年04月08日").get()); assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014年04月08日"));
assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get()); assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("2006-01-02T15:04:05+0000"));
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get()); assertEquals("2009-08-13", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09-07:00"));
assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get()); assertEquals("2009-08-12", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09"));
assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get()); assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.3186369"));
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get()); assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000"));
assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get()); assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.123"));
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get()); assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43"));
assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43").get()); assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43:22"));
assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43:22").get()); assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 UTC"));
assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 UTC").get()); assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 GMT"));
assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 GMT").get()); assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 05:24:37 PM"));
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 05:24:37 PM").get()); assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800"));
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800").get()); assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800 +08"));
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800 +08").get()); assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:44 +09:00"));
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:44 +09:00").get()); assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000 +0000 UTC"));
assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000 +0000 UTC").get()); assertEquals("2015-09-30", GraphCleaningFunctions.cleanDate("2015-09-30 18:48:56.35272715 +0000 UTC"));
assertEquals("2015-09-30", GraphCleaningFunctions.doCleanDate("2015-09-30 18:48:56.35272715 +0000 UTC").get()); assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 GMT"));
assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 GMT").get()); assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 UTC"));
assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 UTC").get());
assertEquals( assertEquals(
"2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00 +0300 MSK m=+0.000000001").get()); "2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00 +0300 MSK m=+0.000000001"));
assertEquals( assertEquals(
"2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001").get()); "2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001"));
assertEquals("2017-07-19", GraphCleaningFunctions.doCleanDate("2017-07-19 03:21:51+00:00").get()); assertEquals("2017-07-19", GraphCleaningFunctions.cleanDate("2017-07-19 03:21:51+00:00"));
assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26").get()); assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26"));
assertEquals("2014-04-01", GraphCleaningFunctions.doCleanDate("2014-04").get()); assertEquals("2014-04-01", GraphCleaningFunctions.cleanDate("2014-04"));
assertEquals("2014-01-01", GraphCleaningFunctions.doCleanDate("2014").get()); assertEquals("2014-01-01", GraphCleaningFunctions.cleanDate("2014"));
assertEquals("2014-05-11", GraphCleaningFunctions.doCleanDate("2014-05-11 08:20:13,787").get()); assertEquals("2014-05-11", GraphCleaningFunctions.cleanDate("2014-05-11 08:20:13,787"));
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3.31.2014").get()); assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3.31.2014"));
assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03.31.2014").get()); assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03.31.2014"));
assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08.21.71").get()); assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08.21.71"));
assertEquals("2014-03-01", GraphCleaningFunctions.doCleanDate("2014.03").get()); assertEquals("2014-03-01", GraphCleaningFunctions.cleanDate("2014.03"));
assertEquals("2014-03-30", GraphCleaningFunctions.doCleanDate("2014.03.30").get()); assertEquals("2014-03-30", GraphCleaningFunctions.cleanDate("2014.03.30"));
assertEquals("2014-06-01", GraphCleaningFunctions.doCleanDate("20140601").get()); assertEquals("2014-06-01", GraphCleaningFunctions.cleanDate("20140601"));
assertEquals("2014-07-22", GraphCleaningFunctions.doCleanDate("20140722105203").get()); assertEquals("2014-07-22", GraphCleaningFunctions.cleanDate("20140722105203"));
assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("1332151919").get()); assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("1332151919"));
assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367189").get()); assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367189"));
assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222").get()); assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222"));
assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222333").get()); assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222333"));
} }

2
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala
View File

@ -284,4 +284,4 @@ object SparkGenerateDoiBoost {
.save(s"$workingDirPath/doiBoostOrganization") .save(s"$workingDirPath/doiBoostOrganization")
} }
} }

14
dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala
View File

@ -280,10 +280,10 @@ case object Crossref2Oaf {
instance.setDateofacceptance(asField(createdDate.getValue)) instance.setDateofacceptance(asField(createdDate.getValue))
} }
val s: List[String] = List("https://doi.org/" + doi) val s: List[String] = List("https://doi.org/" + doi)
// val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct // val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct
// if (links.nonEmpty) { // if (links.nonEmpty) {
// instance.setUrl(links.asJava) // instance.setUrl(links.asJava)
// } // }
if (s.nonEmpty) { if (s.nonEmpty) {
instance.setUrl(s.asJava) instance.setUrl(s.asJava)
} }
@ -584,12 +584,10 @@ case object Crossref2Oaf {
if (dp.length == 10) { if (dp.length == 10) {
return GraphCleaningFunctions.cleanDate(dp) return GraphCleaningFunctions.cleanDate(dp)
} }
} } else if (res.size == 2) {
else if (res.size ==2) {
val dp = f"${res.head}-${res(1)}%02d-01" val dp = f"${res.head}-${res(1)}%02d-01"
return GraphCleaningFunctions.cleanDate(dp) return GraphCleaningFunctions.cleanDate(dp)
} } else if (res.size == 1) {
else if (res.size ==1) {
return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01") return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01")
} }
} }

4
dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala
View File

@ -73,10 +73,10 @@ class CrossrefMappingTest {
} }
@Test @Test
def crossrefIssueDateTest(): Unit = { def crossrefIssueDateTest(): Unit = {
val json = Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString val json =
Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString
assertNotNull(json) assertNotNull(json)
assertFalse(json.isEmpty) assertFalse(json.isEmpty)
val resultList: List[Oaf] = Crossref2Oaf.convert(json) val resultList: List[Oaf] = Crossref2Oaf.convert(json)

94
dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java
View File

@ -27,15 +27,7 @@ import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_PROJECT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT; import static eu.dnetlib.dhp.schema.common.ModelConstants.RESULT_RESULT;
import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE; import static eu.dnetlib.dhp.schema.common.ModelConstants.SOFTWARE_DEFAULT_RESULTTYPE;
import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM; import static eu.dnetlib.dhp.schema.common.ModelConstants.USER_CLAIM;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.asString; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.createOpenaireId;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.dataInfo;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.field;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.journal;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listFields;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.listKeyValues;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier;
import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty;
import java.io.Closeable; import java.io.Closeable;
import java.io.IOException; import java.io.IOException;
@ -143,8 +135,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
smdbe.execute("queryClaims.sql", smdbe::processClaims); smdbe.execute("queryClaims.sql", smdbe::processClaims);
break; break;
case openaire: case openaire:
log.info("Processing datasources..."); log.info("Processing services...");
smdbe.execute("queryDatasources.sql", smdbe::processDatasource, verifyNamespacePrefix); smdbe.execute("queryServices.sql", smdbe::processService, verifyNamespacePrefix);
log.info("Processing projects..."); log.info("Processing projects...");
if (dbSchema.equalsIgnoreCase("beta")) { if (dbSchema.equalsIgnoreCase("beta")) {
@ -156,10 +148,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
log.info("Processing Organizations..."); log.info("Processing Organizations...");
smdbe.execute("queryOrganizations.sql", smdbe::processOrganization, verifyNamespacePrefix); smdbe.execute("queryOrganizations.sql", smdbe::processOrganization, verifyNamespacePrefix);
log.info("Processing relationsNoRemoval ds <-> orgs ..."); log.info("Processing relations services <-> orgs ...");
smdbe smdbe
.execute( .execute(
"queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization, "queryServiceOrganization.sql", smdbe::processServiceOrganization,
verifyNamespacePrefix); verifyNamespacePrefix);
log.info("Processing projects <-> orgs ..."); log.info("Processing projects <-> orgs ...");
@ -235,32 +227,30 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
dbClient.processResults(sql, consumer); dbClient.processResults(sql, consumer);
} }
public List<Oaf> processDatasource(final ResultSet rs) { public List<Oaf> processService(final ResultSet rs) {
try { try {
final DataInfo info = prepareDataInfo(rs); final DataInfo info = prepareDataInfo(rs);
final Datasource ds = new Datasource(); final Datasource ds = new Datasource();
ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); ds.setId(createOpenaireId(10, rs.getString("id"), true));
ds ds
.setOriginalId( .setOriginalId(
Arrays Arrays
.asList((String[]) rs.getArray("identities").getArray()) .asList((String[]) rs.getArray("originalid").getArray())
.stream() .stream()
.filter(StringUtils::isNotBlank) .filter(StringUtils::isNotBlank)
.collect(Collectors.toList())); .collect(Collectors.toList()));
ds ds.setCollectedfrom(prepareCollectedfrom(rs.getArray("collectedfrom")));
.setCollectedfrom( ds.setPid(prepareListOfStructProps(rs.getArray("pid"), info));
listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true),
rs.getString("collectedfromname")));
ds.setPid(new ArrayList<>());
ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateofcollection(asString(rs.getDate("dateofcollection")));
ds.setDateoftransformation(null); // Value not returned by the SQL query ds.setDateoftransformation(null); // Value not returned by the SQL query
ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB
ds.setOaiprovenance(null); // Values not present in the DB ds.setOaiprovenance(null); // Values not present in the DB
ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype")));
ds.setDatasourcetypeui(prepareQualifierSplitting(rs.getString("datasourcetypeui"))); ds.setDatasourcetypeui(prepareQualifierSplitting(rs.getString("datasourcetypeui")));
ds.setEosctype(prepareQualifierSplitting(rs.getString("eosctype")));
ds.setEoscdatasourcetype(prepareQualifierSplitting(rs.getString("eoscdatasourcetype")));
ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility"))); ds.setOpenairecompatibility(prepareQualifierSplitting(rs.getString("openairecompatibility")));
ds.setOfficialname(field(rs.getString("officialname"), info)); ds.setOfficialname(field(rs.getString("officialname"), info));
ds.setEnglishname(field(rs.getString("englishname"), info)); ds.setEnglishname(field(rs.getString("englishname"), info));
@ -277,20 +267,19 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info)); ds.setOdnumberofitemsdate(field(asString(rs.getDate("odnumberofitemsdate")), info));
ds.setOdpolicies(field(rs.getString("odpolicies"), info)); ds.setOdpolicies(field(rs.getString("odpolicies"), info));
ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info)); ds.setOdlanguages(prepareListFields(rs.getArray("odlanguages"), info));
ds.setOdcontenttypes(prepareListFields(rs.getArray("odcontenttypes"), info)); ds.setLanguages(listValues(rs.getArray("languages")));
ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info)); ds.setAccessinfopackage(prepareListFields(rs.getArray("accessinfopackage"), info));
ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); ds.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info));
ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info)); ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), info));
ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info)); ds.setMissionstatementurl(field(rs.getString("missionstatementurl"), info));
ds.setDataprovider(field(rs.getBoolean("dataprovider"), info));
ds.setServiceprovider(field(rs.getBoolean("serviceprovider"), info));
ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info)); ds.setDatabaseaccesstype(field(rs.getString("databaseaccesstype"), info));
ds.setDatauploadtype(field(rs.getString("datauploadtype"), info)); ds.setDatauploadtype(field(rs.getString("datauploadtype"), info));
ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info));
ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info));
ds.setVersioning(field(rs.getBoolean("versioning"), info)); ds.setVersioning(field(rs.getBoolean("versioning"), info));
ds.setVersioncontrol(rs.getBoolean("versioncontrol"));
ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info));
ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info));
ds.setPidsystems(field(rs.getString("pidsystems"), info)); ds.setPidsystems(field(rs.getString("pidsystems"), info));
ds.setCertificates(field(rs.getString("certificates"), info)); ds.setCertificates(field(rs.getString("certificates"), info));
ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array
@ -299,13 +288,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
journal( journal(
rs.getString("officialname"), rs.getString("issnPrinted"), rs.getString("issnOnline"), rs.getString("officialname"), rs.getString("issnPrinted"), rs.getString("issnOnline"),
rs.getString("issnLinking"), info)); // Journal rs.getString("issnLinking"), info)); // Journal
ds.setDataInfo(info);
ds.setLastupdatetimestamp(lastUpdateTimestamp);
ds.setResearchentitytypes(listValues(rs.getArray("researchentitytypes")));
ds.setJurisdiction(prepareQualifierSplitting(rs.getString("jurisdiction"))); ds.setJurisdiction(prepareQualifierSplitting(rs.getString("jurisdiction")));
ds.setThematic(rs.getBoolean("thematic")); ds.setThematic(rs.getBoolean("thematic"));
ds.setKnowledgegraph(rs.getBoolean("knowledgegraph"));
ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies"))); ds.setContentpolicies(prepareListOfQualifiers(rs.getArray("contentpolicies")));
ds.setSubmissionpolicyurl(rs.getString("submissionpolicyurl"));
ds.setPreservationpolicyurl(rs.getString("preservationpolicyurl"));
ds.setResearchproductaccesspolicies(listValues(rs.getArray("researchproductaccesspolicies")));
ds
.setResearchproductmetadataaccesspolicies(
listValues(rs.getArray("researchproductmetadataaccesspolicies")));
ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse")); ds.setConsenttermsofuse(rs.getBoolean("consenttermsofuse"));
ds.setFulltextdownload(rs.getBoolean("fulltextdownload")); ds.setFulltextdownload(rs.getBoolean("fulltextdownload"));
ds ds
@ -313,8 +307,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
Optional Optional
.ofNullable( .ofNullable(
rs.getDate("consenttermsofusedate")) rs.getDate("consenttermsofusedate"))
.map(c -> c.toString()) .map(java.sql.Date::toString)
.orElse(null)); .orElse(null));
ds
.setLastconsenttermsofusedate(
Optional
.ofNullable(
rs.getDate("lastconsenttermsofusedate"))
.map(java.sql.Date::toString)
.orElse(null));
ds.setDataInfo(info);
ds.setLastupdatetimestamp(lastUpdateTimestamp);
return Arrays.asList(ds); return Arrays.asList(ds);
} catch (final Exception e) { } catch (final Exception e) {
@ -425,11 +429,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
} }
} }
public List<Oaf> processDatasourceOrganization(final ResultSet rs) { public List<Oaf> processServiceOrganization(final ResultSet rs) {
try { try {
final DataInfo info = prepareDataInfo(rs); final DataInfo info = prepareDataInfo(rs);
final String orgId = createOpenaireId(20, rs.getString("organization"), true); final String orgId = createOpenaireId(20, rs.getString("organization"), true);
final String dsId = createOpenaireId(10, rs.getString("datasource"), true); final String dsId = createOpenaireId(10, rs.getString("service"), true);
final List<KeyValue> collectedFrom = listKeyValues( final List<KeyValue> collectedFrom = listKeyValues(
createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname"));
@ -603,6 +607,32 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i
String.format("%.3f", trust)); String.format("%.3f", trust));
} }
private List<KeyValue> prepareCollectedfrom(Array values) throws SQLException {
if (Objects.isNull(values)) {
return null;
}
return Arrays
.stream((String[]) values.getArray())
.filter(Objects::nonNull)
.distinct()
.map(s -> keyValueSplitting(s, "@@@"))
.collect(Collectors.toList());
}
public static KeyValue keyValueSplitting(final String s, String separator) {
if (StringUtils.isBlank(s)) {
return null;
}
final String[] arr = s.split(separator);
if (arr.length != 2) {
return null;
}
KeyValue kv = new KeyValue();
kv.setKey(createOpenaireId(10, arr[0], true));
kv.setValue(arr[1]);
return kv;
}
private Qualifier prepareQualifierSplitting(final String s) { private Qualifier prepareQualifierSplitting(final String s) {
if (StringUtils.isBlank(s)) { if (StringUtils.isBlank(s)) {
return null; return null;

65
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml
View File

@ -30,6 +30,11 @@
<value></value> <value></value>
<description>a blacklist of nsprefixes (comma separeted)</description> <description>a blacklist of nsprefixes (comma separeted)</description>
</property> </property>
<property>
<name>reuseContent</name>
<value>false</value>
<description>reuse content in the aggregator database</description>
</property>
<property> <property>
<name>sparkDriverMemory</name> <name>sparkDriverMemory</name>
<description>memory for driver process</description> <description>memory for driver process</description>
@ -85,12 +90,20 @@
</configuration> </configuration>
</global> </global>
<start to="ImportDB"/> <start to="reuse_db"/>
<kill name="Kill"> <kill name="Kill">
<message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message> <message>Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}]</message>
</kill> </kill>
<decision name="reuse_db">
<switch>
<case to="ImportDB">${wf:conf('reuseContent') eq false}</case>
<case to="GenerateEntities">${wf:conf('reuseContent') eq true}</case>
<default to="ImportDB"/>
</switch>
</decision>
<action name="ImportDB"> <action name="ImportDB">
<java> <java>
<prepare> <prepare>
@ -102,6 +115,7 @@
<arg>--postgresUser</arg><arg>${postgresUser}</arg> <arg>--postgresUser</arg><arg>${postgresUser}</arg>
<arg>--postgresPassword</arg><arg>${postgresPassword}</arg> <arg>--postgresPassword</arg><arg>${postgresPassword}</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg> <arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--action</arg><arg>openaire</arg>
<arg>--dbschema</arg><arg>${dbSchema}</arg> <arg>--dbschema</arg><arg>${dbSchema}</arg>
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg> <arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
</java> </java>
@ -124,6 +138,55 @@
<arg>--action</arg><arg>claims</arg> <arg>--action</arg><arg>claims</arg>
<arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg> <arg>--nsPrefixBlacklist</arg><arg>${nsPrefixBlacklist}</arg>
</java> </java>
<ok to="GenerateEntities"/>
<error to="Kill"/>
</action>
<action name="GenerateEntities">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>GenerateEntities</name>
<class>eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--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}${spark2EventLogDir}
</spark-opts>
<arg>--sourcePaths</arg><arg>${contentPath}/db_records,${contentPath}/db_claims</arg>
<arg>--targetPath</arg><arg>${workingDir}/entities</arg>
<arg>--isLookupUrl</arg><arg>${isLookupUrl}</arg>
<arg>--shouldHashId</arg><arg>true</arg>
</spark>
<ok to="GenerateGraph"/>
<error to="Kill"/>
</action>
<action name="GenerateGraph">
<spark xmlns="uri:oozie:spark-action:0.2">
<master>yarn</master>
<mode>cluster</mode>
<name>GenerateGraph</name>
<class>eu.dnetlib.dhp.oa.graph.raw.DispatchEntitiesApplication</class>
<jar>dhp-graph-mapper-${projectVersion}.jar</jar>
<spark-opts>
--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}${spark2EventLogDir}
--conf spark.sql.shuffle.partitions=7680
</spark-opts>
<arg>--sourcePath</arg><arg>${workingDir}/entities</arg>
<arg>--graphRawPath</arg><arg>${workingDir}/graph_aggregator</arg>
</spark>
<ok to="End"/> <ok to="End"/>
<error to="Kill"/> <error to="Kill"/>
</action> </action>

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql
View File

@ -27,7 +27,7 @@ SELECT
'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction,
array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid
FROM dsm_organizations o FROM dsm_organizations o
LEFT OUTER JOIN dsm_datasources d ON (d.id = o.collectedfrom) LEFT OUTER JOIN dsm_services d ON (d.id = o.collectedfrom)
LEFT OUTER JOIN dsm_organizationpids p ON (p.organization = o.id) LEFT OUTER JOIN dsm_organizationpids p ON (p.organization = o.id)
LEFT OUTER JOIN dsm_identities i ON (i.pid = p.pid) LEFT OUTER JOIN dsm_identities i ON (i.pid = p.pid)
GROUP BY GROUP BY

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql
View File

@ -16,4 +16,4 @@ SELECT
FROM project_organization po FROM project_organization po
LEFT OUTER JOIN projects p ON (p.id = po.project) LEFT OUTER JOIN projects p ON (p.id = po.project)
LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom); LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom);

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql
View File

@ -42,7 +42,7 @@ SELECT
LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) LEFT OUTER JOIN projectpids pp ON (pp.project = p.id)
LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid)
LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom) LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom)
LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id) LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id)
LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding) LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding)

2
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql
View File

@ -40,7 +40,7 @@ SELECT
LEFT OUTER JOIN projectpids pp ON (pp.project = p.id) LEFT OUTER JOIN projectpids pp ON (pp.project = p.id)
LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid) LEFT OUTER JOIN dsm_identities i ON (i.pid = pp.pid)
LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom) LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom)
LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id) LEFT OUTER JOIN project_fundingpath pf ON (pf.project = p.id)
LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding) LEFT OUTER JOIN fundingpaths fp ON (fp.id = pf.funding)

8
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql
View File

@ -1,5 +1,5 @@
SELECT SELECT
dor.datasource AS datasource, dor.service AS service,
dor.organization AS organization, dor.organization AS organization,
NULL AS startdate, NULL AS startdate,
NULL AS enddate, NULL AS enddate,
@ -11,6 +11,6 @@ SELECT
dc.officialname AS collectedfromname, dc.officialname AS collectedfromname,
'providedBy@@@dnet:datasources_organizations_typologies' AS semantics, 'providedBy@@@dnet:datasources_organizations_typologies' AS semantics,
d.provenanceaction || '@@@dnet:provenanceActions' AS provenanceaction d.provenanceaction || '@@@dnet:provenanceActions' AS provenanceaction
FROM dsm_datasource_organization dor FROM dsm_service_organization dor
LEFT OUTER JOIN dsm_datasources d ON (dor.datasource = d.id) LEFT OUTER JOIN dsm_services d ON (dor.service = d.id)
LEFT OUTER JOIN dsm_datasources dc ON (dc.id = d.collectedfrom); LEFT OUTER JOIN dsm_services dc ON (dc.id = d.collectedfrom);

107
dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql → dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql
View File

@ -1,6 +1,7 @@
SELECT SELECT
d.id AS datasourceid, d.id AS id,
d.id || array_agg(distinct di.pid) AS identities, array_remove(d.id || array_agg(distinct CASE WHEN dp.pid like 'piwik%' THEN di.pid ELSE NULL END) || array_agg(distinct dds.duplicate), NULL) AS originalid,
array_remove(array_agg(distinct CASE WHEN di.pid NOT LIKE 'piwik%' THEN di.pid||'###'||di.issuertype||'@@@'||'dnet:pid_types' ELSE NULL END), NULL) as pid,
d.officialname AS officialname, d.officialname AS officialname,
d.englishname AS englishname, d.englishname AS englishname,
d.contactemail AS contactemail, d.contactemail AS contactemail,
@ -9,8 +10,8 @@ SELECT
THEN THEN
'openaire-cris_1.1@@@dnet:datasourceCompatibilityLevel' 'openaire-cris_1.1@@@dnet:datasourceCompatibilityLevel'
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire4.0']) WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire4.0'])
THEN THEN
'openaire4.0@@@dnet:datasourceCompatibilityLevel' 'openaire4.0@@@dnet:datasourceCompatibilityLevel'
WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0']) WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0'])
THEN THEN
'driver-openaire2.0@@@dnet:datasourceCompatibilityLevel' 'driver-openaire2.0@@@dnet:datasourceCompatibilityLevel'
@ -40,25 +41,29 @@ SELECT
END AS openairecompatibility, END AS openairecompatibility,
d.websiteurl AS websiteurl, d.websiteurl AS websiteurl,
d.logourl AS logourl, d.logourl AS logourl,
array_agg(DISTINCT CASE WHEN a.protocol = 'oai' and last_aggregation_date is not null THEN a.baseurl ELSE NULL END) AS accessinfopackage, array_remove(array_agg(DISTINCT CASE WHEN a.protocol = 'oai' and last_aggregation_date is not null THEN a.baseurl ELSE NULL END), NULL) AS accessinfopackage,
d.latitude AS latitude, d.latitude AS latitude,
d.longitude AS longitude, d.longitude AS longitude,
d.namespaceprefix AS namespaceprefix, d.namespaceprefix AS namespaceprefix,
NULL AS odnumberofitems, NULL AS odnumberofitems,
NULL AS odnumberofitemsdate, NULL AS odnumberofitemsdate,
(SELECT array_agg(s|| '###keywords@@@dnet:subject_classification_typologies') (SELECT array_agg(s|| '###keywords@@@dnet:subject_classification_typologies')
FROM UNNEST( FROM UNNEST(
ARRAY( ARRAY(
SELECT trim(s) SELECT trim(s)
FROM unnest(string_to_array(d.subjects, '@@')) AS s)) AS s) AS subjects, FROM unnest(string_to_array(d.subjects, '@@')) AS s)) AS s) AS subjects,
d.description AS description, d.description AS description,
NULL AS odpolicies, NULL AS odpolicies,
ARRAY(SELECT trim(s) array_remove(ARRAY(SELECT trim(s)
FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g'), ',')) AS s), '{}') AS odlanguages,
ARRAY(SELECT trim(s) array_remove(ARRAY(SELECT trim(s)
FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g'), ',')) AS s), '{}') AS languages,
-- Term provided only by OpenDOAR:
-- probably updating the TR it could be replaced by research_entity_types[]
-- But a study on the vocabulary terms is needed
-- REMOVED: ARRAY(SELECT trim(s) FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes,
false AS inferred, false AS inferred,
false AS deletedbyinference, false AS deletedbyinference,
0.9 AS trust, 0.9 AS trust,
@ -69,39 +74,59 @@ SELECT
d.releasestartdate AS releasestartdate, d.releasestartdate AS releasestartdate,
d.releaseenddate AS releaseenddate, d.releaseenddate AS releaseenddate,
d.missionstatementurl AS missionstatementurl, d.missionstatementurl AS missionstatementurl,
d.dataprovider AS dataprovider, -- the following 2 fields (provided by re3data) have been replaced by research_entity_types[]
d.serviceprovider AS serviceprovider, -- VALUE 'Research Data' : d.dataprovider AS dataprovider,
-- VALUE 'Services' : d.serviceprovider AS serviceprovider,
d.databaseaccesstype AS databaseaccesstype, d.databaseaccesstype AS databaseaccesstype,
d.datauploadtype AS datauploadtype, d.datauploadtype AS datauploadtype,
d.databaseaccessrestriction AS databaseaccessrestriction, d.databaseaccessrestriction AS databaseaccessrestriction,
d.datauploadrestriction AS datauploadrestriction, d.datauploadrestriction AS datauploadrestriction,
d.versioning AS versioning, -- REPLACED BY version_control : d.versioning AS versioning,
d.version_control AS versioning,
d.version_control AS versioncontrol,
d.citationguidelineurl AS citationguidelineurl, d.citationguidelineurl AS citationguidelineurl,
d.qualitymanagementkind AS qualitymanagementkind, array_to_string(array_agg(distinct dps.scheme), ' ') AS pidsystems,
d.pidsystems AS pidsystems,
d.certificates AS certificates, d.certificates AS certificates,
ARRAY[]::text[] AS policies, ARRAY[]::text[] AS policies,
dc.id AS collectedfromid, array_remove(
dc.officialname AS collectedfromname, array(
d.typology||'@@@dnet:datasource_typologies' AS datasourcetype, select distinct cf
d.typology||'@@@dnet:datasource_typologies_ui' AS datasourcetypeui, from unnest(
'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, dc.id||'@@@'||dc.officialname || array_agg(distinct dds_cf.id||'@@@'||dds_cf.officialname)
) as cf),
NULL) AS collectedfrom,
d._typology_to_remove_||'@@@dnet:datasource_typologies' AS datasourcetype,
d._typology_to_remove_||'@@@dnet:datasource_typologies_ui' AS datasourcetypeui,
d.eosc_type||'@@@dnet:eosc_types' AS eosctype,
d.eosc_datasource_type||'@@@dnet:eosc_datasource_types' AS eoscdatasourcetype,
d.issn AS issnPrinted, d.issn AS issnPrinted,
d.eissn AS issnOnline, d.eissn AS issnOnline,
d.lissn AS issnLinking, d.lissn AS issnLinking,
d.research_entity_types AS researchentitytypes,
d.consenttermsofuse AS consenttermsofuse, d.consenttermsofuse AS consenttermsofuse,
d.fulltextdownload AS fulltextdownload, d.fulltextdownload AS fulltextdownload,
d.consenttermsofusedate AS consenttermsofusedate, d.consenttermsofusedate AS consenttermsofusedate,
de.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, d.lastconsenttermsofusedate AS lastconsenttermsofusedate,
de.thematic AS thematic, d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction,
de.knowledge_graph AS knowledgegraph, d.thematic AS thematic,
array(select unnest(de.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies array(select unnest(d.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies,
nullif(trim(d.submission_policy_url), '') AS submissionpolicyurl,
nullif(trim(d.preservation_policy_url), '') AS preservationpolicyurl,
array_remove(d.research_product_access_policies, '') AS researchproductaccesspolicies,
array_remove(d.research_product_metadata_access_policies, '') AS researchproductmetadataaccesspolicies
FROM dsm_datasources d FROM dsm_services d
LEFT OUTER JOIN dsm_datasources_eosc de on (d.id = de.id) LEFT OUTER JOIN dsm_services dc on (d.collectedfrom = dc.id)
LEFT OUTER JOIN dsm_datasources dc on (d.collectedfrom = dc.id) LEFT OUTER JOIN dsm_api a ON (d.id = a.service)
LEFT OUTER JOIN dsm_api a ON (d.id = a.datasource) LEFT OUTER JOIN dsm_servicepids dp ON (d.id = dp.service)
LEFT OUTER JOIN dsm_datasourcepids di ON (d.id = di.datasource) LEFT OUTER JOIN dsm_identities di ON (dp.pid = di.pid)
LEFT OUTER JOIN dsm_dedup_services dds ON (d.id = dds.id)
LEFT OUTER JOIN dsm_services dds_dup ON (dds.duplicate = dds_dup.id)
LEFT OUTER JOIN dsm_services dds_cf ON (dds_dup.collectedfrom = dds_cf.id)
LEFT OUTER JOIN dsm_pid_systems dps ON (d.id = dps.service)
WHERE
d.dedup_main_service = true
GROUP BY GROUP BY
d.id, d.id,
@ -119,23 +144,27 @@ GROUP BY
d.releasestartdate, d.releasestartdate,
d.releaseenddate, d.releaseenddate,
d.missionstatementurl, d.missionstatementurl,
d.dataprovider, -- TODO REMOVED ???: d.dataprovider,
d.serviceprovider, -- TODO REMOVED ???: d.serviceprovider,
d.databaseaccesstype, d.databaseaccesstype,
d.datauploadtype, d.datauploadtype,
d.databaseaccessrestriction, d.databaseaccessrestriction,
d.datauploadrestriction, d.datauploadrestriction,
d.versioning, -- REPLACED BY version_control : d.versioning,
d.version_control,
d.citationguidelineurl, d.citationguidelineurl,
d.qualitymanagementkind, -- REMOVED: d.qualitymanagementkind,
d.pidsystems,
d.certificates, d.certificates,
dc.id, dc.id,
dc.officialname, dc.officialname,
d.issn, d.issn,
d.eissn, d.eissn,
d.lissn, d.lissn,
de.jurisdiction, d.jurisdiction,
de.thematic, d.thematic,
de.knowledge_graph, -- REMOVED ???: de.knowledge_graph,
de.content_policies d.content_policies,
d.submission_policy_url,
d.preservation_policy_url,
d.research_product_access_policies,
d.research_product_metadata_access_policies

146
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java
View File

@ -12,8 +12,11 @@ import java.sql.Array;
import java.sql.Date; import java.sql.Date;
import java.sql.ResultSet; import java.sql.ResultSet;
import java.sql.SQLException; import java.sql.SQLException;
import java.util.HashSet;
import java.util.List; import java.util.List;
import java.util.Objects; import java.util.Objects;
import java.util.Optional;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils; import org.apache.commons.lang3.StringUtils;
@ -28,12 +31,7 @@ import com.fasterxml.jackson.core.type.TypeReference;
import com.fasterxml.jackson.databind.ObjectMapper; import com.fasterxml.jackson.databind.ObjectMapper;
import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup;
import eu.dnetlib.dhp.schema.oaf.Datasource; import eu.dnetlib.dhp.schema.oaf.*;
import eu.dnetlib.dhp.schema.oaf.Oaf;
import eu.dnetlib.dhp.schema.oaf.Organization;
import eu.dnetlib.dhp.schema.oaf.Project;
import eu.dnetlib.dhp.schema.oaf.Relation;
import eu.dnetlib.dhp.schema.oaf.Result;
import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils;
@ExtendWith(MockitoExtension.class) @ExtendWith(MockitoExtension.class)
@ -63,22 +61,32 @@ public class MigrateDbEntitiesApplicationTest {
} }
@Test @Test
public void testProcessDatasource() throws Exception { public void testProcessService() throws Exception {
final List<TypedField> fields = prepareMocks("datasources_resultset_entry.json"); final List<TypedField> fields = prepareMocks("services_resultset_entry.json");
final List<Oaf> list = app.processDatasource(rs); final List<Oaf> list = app.processService(rs);
assertEquals(1, list.size()); assertEquals(1, list.size());
verifyMocks(fields); verifyMocks(fields);
final Datasource ds = (Datasource) list.get(0); final Datasource ds = (Datasource) list.get(0);
assertValidId(ds.getId()); assertValidId(ds.getId());
assertValidId(ds.getCollectedfrom().get(0).getKey()); ds
.getCollectedfrom()
.stream()
.map(KeyValue::getKey)
.forEach(dsId -> assertValidId(dsId));
assertEquals(1, ds.getPid().size());
assertEquals("r3d100010218", ds.getPid().get(0).getValue());
assertEquals("re3data", ds.getPid().get(0).getQualifier().getClassid());
assertEquals("dnet:pid_types", ds.getPid().get(0).getQualifier().getSchemeid());
assertEquals(getValueAsString("officialname", fields), ds.getOfficialname().getValue()); assertEquals(getValueAsString("officialname", fields), ds.getOfficialname().getValue());
assertEquals(getValueAsString("englishname", fields), ds.getEnglishname().getValue()); assertEquals(getValueAsString("englishname", fields), ds.getEnglishname().getValue());
assertEquals(getValueAsString("contactemail", fields), ds.getContactemail().getValue());
assertEquals(getValueAsString("websiteurl", fields), ds.getWebsiteurl().getValue()); assertEquals(getValueAsString("websiteurl", fields), ds.getWebsiteurl().getValue());
assertEquals(getValueAsString("logourl", fields), ds.getLogourl());
assertEquals(getValueAsString("contactemail", fields), ds.getContactemail().getValue());
assertEquals(getValueAsString("namespaceprefix", fields), ds.getNamespaceprefix().getValue()); assertEquals(getValueAsString("namespaceprefix", fields), ds.getNamespaceprefix().getValue());
assertEquals(getValueAsString("collectedfromname", fields), ds.getCollectedfrom().get(0).getValue());
assertEquals(getValueAsString("officialname", fields), ds.getJournal().getName()); assertEquals(getValueAsString("officialname", fields), ds.getJournal().getName());
assertEquals(getValueAsString("issnPrinted", fields), ds.getJournal().getIssnPrinted()); assertEquals(getValueAsString("issnPrinted", fields), ds.getJournal().getIssnPrinted());
assertEquals(getValueAsString("issnOnline", fields), ds.getJournal().getIssnOnline()); assertEquals(getValueAsString("issnOnline", fields), ds.getJournal().getIssnOnline());
@ -90,19 +98,98 @@ public class MigrateDbEntitiesApplicationTest {
assertEquals("pubsrepository::journal", ds.getDatasourcetypeui().getClassid()); assertEquals("pubsrepository::journal", ds.getDatasourcetypeui().getClassid());
assertEquals("dnet:datasource_typologies_ui", ds.getDatasourcetypeui().getSchemeid()); assertEquals("dnet:datasource_typologies_ui", ds.getDatasourcetypeui().getSchemeid());
assertEquals("Data Source", ds.getEosctype().getClassid());
assertEquals("Data Source", ds.getEosctype().getClassname());
assertEquals("dnet:eosc_types", ds.getEosctype().getSchemeid());
assertEquals("dnet:eosc_types", ds.getEosctype().getSchemename());
assertEquals("Journal archive", ds.getEoscdatasourcetype().getClassid());
assertEquals("Journal archive", ds.getEoscdatasourcetype().getClassname());
assertEquals("dnet:eosc_datasource_types", ds.getEoscdatasourcetype().getSchemeid());
assertEquals("dnet:eosc_datasource_types", ds.getEoscdatasourcetype().getSchemename());
assertEquals("openaire4.0", ds.getOpenairecompatibility().getClassid());
assertEquals("openaire4.0", ds.getOpenairecompatibility().getClassname());
assertEquals("dnet:datasourceCompatibilityLevel", ds.getOpenairecompatibility().getSchemeid());
assertEquals("dnet:datasourceCompatibilityLevel", ds.getOpenairecompatibility().getSchemename());
assertEquals(getValueAsDouble("latitude", fields).toString(), ds.getLatitude().getValue());
assertEquals(getValueAsDouble("longitude", fields).toString(), ds.getLongitude().getValue());
assertEquals(getValueAsString("dateofvalidation", fields), ds.getDateofvalidation());
assertEquals(getValueAsString("description", fields), ds.getDescription().getValue());
// TODO assertEquals(getValueAsString("subjects", fields), ds.getSubjects());
assertEquals("0.0", ds.getOdnumberofitems().getValue());
assertEquals(getValueAsString("odnumberofitemsdate", fields), ds.getOdnumberofitemsdate());
assertEquals(getValueAsString("odpolicies", fields), ds.getOdpolicies());
assertEquals(
getValueAsList("odlanguages", fields),
ds.getOdlanguages().stream().map(Field::getValue).collect(Collectors.toList()));
assertEquals(getValueAsList("languages", fields), ds.getLanguages());
assertEquals(
getValueAsList("accessinfopackage", fields),
ds.getAccessinfopackage().stream().map(Field::getValue).collect(Collectors.toList()));
assertEquals(getValueAsString("releasestartdate", fields), ds.getReleasestartdate());
assertEquals(getValueAsString("releaseenddate", fields), ds.getReleasestartdate());
assertEquals(getValueAsString("missionstatementurl", fields), ds.getMissionstatementurl());
assertEquals(false, ds.getDataprovider().getValue());
assertEquals(false, ds.getServiceprovider().getValue());
assertEquals(getValueAsString("databaseaccesstype", fields), ds.getDatabaseaccesstype());
assertEquals(getValueAsString("datauploadtype", fields), ds.getDatauploadtype());
assertEquals(getValueAsString("databaseaccessrestriction", fields), ds.getDatabaseaccessrestriction());
assertEquals(getValueAsString("datauploadrestriction", fields), ds.getDatauploadrestriction());
assertEquals(false, ds.getVersioning().getValue());
assertEquals(false, ds.getVersioncontrol());
assertEquals(getValueAsString("citationguidelineurl", fields), ds.getCitationguidelineurl());
assertEquals(getValueAsString("pidsystems", fields), ds.getPidsystems());
assertEquals(getValueAsString("certificates", fields), ds.getCertificates());
assertEquals(getValueAsList("researchentitytypes", fields), ds.getResearchentitytypes());
assertEquals("National", ds.getJurisdiction().getClassid()); assertEquals("National", ds.getJurisdiction().getClassid());
assertEquals("eosc:jurisdictions", ds.getJurisdiction().getSchemeid()); assertEquals("eosc:jurisdictions", ds.getJurisdiction().getSchemeid());
assertTrue(ds.getThematic()); assertTrue(ds.getThematic());
assertTrue(ds.getKnowledgegraph());
assertEquals(1, ds.getContentpolicies().size()); HashSet<String> cpSchemeId = ds
assertEquals("Journal article", ds.getContentpolicies().get(0).getClassid()); .getContentpolicies()
assertEquals("eosc:contentpolicies", ds.getContentpolicies().get(0).getSchemeid()); .stream()
.map(Qualifier::getSchemeid)
.collect(Collectors.toCollection(HashSet::new));
assertTrue(cpSchemeId.size() == 1);
assertTrue(cpSchemeId.contains("eosc:contentpolicies"));
HashSet<String> cpSchemeName = ds
.getContentpolicies()
.stream()
.map(Qualifier::getSchemename)
.collect(Collectors.toCollection(HashSet::new));
assertTrue(cpSchemeName.size() == 1);
assertTrue(cpSchemeName.contains("eosc:contentpolicies"));
assertEquals(2, ds.getContentpolicies().size());
assertEquals("Taxonomic classification", ds.getContentpolicies().get(0).getClassid());
assertEquals("Resource collection", ds.getContentpolicies().get(1).getClassid());
assertEquals(getValueAsString("submissionpolicyurl", fields), ds.getSubmissionpolicyurl());
assertEquals(getValueAsString("preservationpolicyurl", fields), ds.getPreservationpolicyurl());
assertEquals(
getValueAsList("researchproductaccesspolicies", fields),
ds.getResearchproductaccesspolicies());
assertEquals(
getValueAsList("researchproductmetadataaccesspolicies", fields),
ds.getResearchproductmetadataaccesspolicies());
assertEquals(true, ds.getConsenttermsofuse()); assertEquals(true, ds.getConsenttermsofuse());
assertEquals(true, ds.getFulltextdownload()); assertEquals(true, ds.getFulltextdownload());
assertEquals("2022-03-11", ds.getConsenttermsofusedate()); assertEquals("2022-03-11", ds.getConsenttermsofusedate());
assertEquals("2022-03-11", ds.getLastconsenttermsofusedate());
} }
@Test @Test
@ -154,7 +241,7 @@ public class MigrateDbEntitiesApplicationTest {
public void testProcessDatasourceOrganization() throws Exception { public void testProcessDatasourceOrganization() throws Exception {
final List<TypedField> fields = prepareMocks("datasourceorganization_resultset_entry.json"); final List<TypedField> fields = prepareMocks("datasourceorganization_resultset_entry.json");
final List<Oaf> list = app.processDatasourceOrganization(rs); final List<Oaf> list = app.processServiceOrganization(rs);
assertEquals(2, list.size()); assertEquals(2, list.size());
verifyMocks(fields); verifyMocks(fields);
@ -356,18 +443,31 @@ public class MigrateDbEntitiesApplicationTest {
} }
private Float getValueAsFloat(final String name, final List<TypedField> fields) { private Float getValueAsFloat(final String name, final List<TypedField> fields) {
return new Float(getValueAs(name, fields).toString()); final Object value = getValueAs(name, fields);
return value != null ? new Float(value.toString()) : null;
}
private Double getValueAsDouble(final String name, final List<TypedField> fields) {
final Object value = getValueAs(name, fields);
return value != null ? new Double(value.toString()) : null;
}
private Integer getValueAsInt(final String name, final List<TypedField> fields) {
final Object value = getValueAs(name, fields);
return value != null ? new Integer(value.toString()) : null;
} }
private <T> T getValueAs(final String name, final List<TypedField> fields) { private <T> T getValueAs(final String name, final List<TypedField> fields) {
return fields final Optional<T> field = fields
.stream() .stream()
.filter(f -> f.getField().equals(name)) .filter(f -> f.getField().equals(name))
.map(TypedField::getValue)
.filter(Objects::nonNull)
.map(o -> (T) o)
.findFirst() .findFirst()
.get(); .map(TypedField::getValue)
.map(o -> (T) o);
if (!field.isPresent()) {
return null;
}
return field.get();
} }
private List<String> getValueAsList(final String name, final List<TypedField> fields) { private List<String> getValueAsList(final String name, final List<TypedField> fields) {

238
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json → dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json
View File

@ -5,14 +5,47 @@
"value": "274269ac6f3b::2579-5449" "value": "274269ac6f3b::2579-5449"
}, },
{ {
"field": "identities", "field": "originalid",
"type": "array", "type": "array",
"value": [ "value": [
"274269ac6f3b::2579-5449", "fairsharing_::1562",
"piwik:13", "piwik:13",
null null,
"re3data_____::r3d100010213"
] ]
}, },
{
"field": "pid",
"type": "array",
"value": [
"r3d100010218###re3data@@@dnet:pid_types"
]
},
{
"field": "datasourcetype",
"type": "string",
"value": "pubsrepository::journal@@@dnet:datasource_typologies"
},
{
"field": "datasourcetypeui",
"type": "string",
"value": "pubsrepository::journal@@@dnet:datasource_typologies_ui"
},
{
"field": "eosctype",
"type": "string",
"value": "Data Source@@@dnet:eosc_types"
},
{
"field": "eoscdatasourcetype",
"type": "string",
"value": "Journal archive@@@dnet:eosc_datasource_types"
},
{
"field": "openairecompatibility",
"type": "string",
"value": "openaire4.0@@@dnet:datasourceCompatibilityLevel"
},
{ {
"field": "officialname", "field": "officialname",
"type": "string", "type": "string",
@ -23,16 +56,6 @@
"type": "string", "type": "string",
"value": "Jurnal Ilmiah Pendidikan Scholastic" "value": "Jurnal Ilmiah Pendidikan Scholastic"
}, },
{
"field": "contactemail",
"type": "string",
"value": "test@test.it"
},
{
"field": "openairecompatibility",
"type": "string",
"value": "hostedBy@@@dnet:datasourceCompatibilityLevel"
},
{ {
"field": "websiteurl", "field": "websiteurl",
"type": "string", "type": "string",
@ -44,11 +67,14 @@
"value": null "value": null
}, },
{ {
"field": "accessinfopackage", "field": "contactemail",
"type": "array", "type": "string",
"value": [ "value": "test@test.it"
null },
] {
"field": "namespaceprefix",
"type": "string",
"value": "ojs_25795449"
}, },
{ {
"field": "latitude", "field": "latitude",
@ -61,9 +87,19 @@
"value": 0 "value": 0
}, },
{ {
"field": "namespaceprefix", "field": "dateofvalidation",
"type": "date",
"value": null
},
{
"field": "description",
"type": "string", "type": "string",
"value": "ojs_25795449" "value": "veterinary medicine"
},
{
"field": "subjects",
"type": "array",
"value": []
}, },
{ {
"field": "odnumberofitems", "field": "odnumberofitems",
@ -75,16 +111,6 @@
"type": "date", "type": "date",
"value": null "value": null
}, },
{
"field": "subjects",
"type": "array",
"value": null
},
{
"field": "description",
"type": "string",
"value": null
},
{ {
"field": "odpolicies", "field": "odpolicies",
"type": "string", "type": "string",
@ -93,44 +119,33 @@
{ {
"field": "odlanguages", "field": "odlanguages",
"type": "array", "type": "array",
"value": []
},
{
"field": "odcontenttypes",
"type": "array",
"value": [ "value": [
"Journal articles" "English",
"German",
"French",
"Danish",
"Norwegian",
"Swedish"
] ]
}, },
{ {
"field": "inferred", "field": "languages",
"type": "boolean", "type": "array",
"value": false "value": [
"English",
"German",
"French",
"Danish",
"Norwegian",
"Swedish"
]
}, },
{ {
"field": "deletedbyinference", "field": "accessinfopackage",
"type": "boolean", "type": "array",
"value": false "value": [
}, "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai"
{ ]
"field": "trust",
"type": "double",
"value": 0.9
},
{
"field": "inferenceprovenance",
"type": "string",
"value": null
},
{
"field": "dateofcollection",
"type": "date",
"value": "2020-01-21"
},
{
"field": "dateofvalidation",
"type": "date",
"value": null
}, },
{ {
"field": "releasestartdate", "field": "releasestartdate",
@ -147,16 +162,6 @@
"type": "string", "type": "string",
"value": null "value": null
}, },
{
"field": "dataprovider",
"type": "boolean",
"value": null
},
{
"field": "serviceprovider",
"type": "boolean",
"value": null
},
{ {
"field": "databaseaccesstype", "field": "databaseaccesstype",
"type": "string", "type": "string",
@ -183,12 +188,12 @@
"value": null "value": null
}, },
{ {
"field": "citationguidelineurl", "field": "versioncontrol",
"type": "string", "type": "boolean",
"value": null "value": null
}, },
{ {
"field": "qualitymanagementkind", "field": "citationguidelineurl",
"type": "string", "type": "string",
"value": null "value": null
}, },
@ -208,29 +213,38 @@
"value": [] "value": []
}, },
{ {
"field": "collectedfromid", "field": "inferred",
"type": "string", "type": "boolean",
"value": "openaire____::SnVybmFsIEZha3VsdGFzIFNhc3RyYSBVbml2ZXJzaXRhcyBFa2FzYWt0aQ==" "value": false
}, },
{ {
"field": "collectedfromname", "field": "deletedbyinference",
"type": "string", "type": "boolean",
"value": "Jurnal Fakultas Sastra Universitas Ekasakti" "value": false
}, },
{ {
"field": "datasourcetype", "field": "trust",
"type": "string", "type": "double",
"value": "pubsrepository::journal@@@dnet:datasource_typologies" "value": 0.9
}, },
{ {
"field": "datasourcetypeui", "field": "inferenceprovenance",
"type": "string", "type": "string",
"value": "pubsrepository::journal@@@dnet:datasource_typologies_ui" "value": null
}, },
{ {
"field": "provenanceaction", "field": "dateofcollection",
"type": "not_used", "type": "date",
"value": "sysimport:crosswalk:entityregistry@@@dnet:provenance_actions" "value": "2020-01-21"
},
{
"field": "collectedfrom",
"type": "array",
"value": [
"openaire____::fairsharing@@@FAIRsharing.org",
"openaire____::opendoar@@@OpenDOAR",
"openaire____::re3data@@@Registry of Research Data Repository"
]
}, },
{ {
"field": "issnPrinted", "field": "issnPrinted",
@ -247,6 +261,20 @@
"type": "string", "type": "string",
"value": "2579-5447" "value": "2579-5447"
}, },
{
"field": "researchentitytypes",
"type": "array",
"value": [
"Research Data"
]
},
{
"field": "providedproducttypes",
"type": "array",
"value": [
]
},
{ {
"field": "jurisdiction", "field": "jurisdiction",
"type": "string", "type": "string",
@ -266,7 +294,32 @@
"field": "contentpolicies", "field": "contentpolicies",
"type": "array", "type": "array",
"value": [ "value": [
"Journal article@@@eosc:contentpolicies" "Taxonomic classification@@@eosc:contentpolicies",
"Resource collection@@@eosc:contentpolicies"
]
},
{
"field": "submissionpolicyurl",
"type": "string",
"value": null
},
{
"field": "preservationpolicyurl",
"type": "string",
"value": "Permanent Archiving https://datadryad.org/stash/faq"
},
{
"field": "researchproductaccesspolicies",
"type": "array",
"value": [
"https://100percentit.com/legal/"
]
},
{
"field": "researchproductmetadataaccesspolicies",
"type": "array",
"value": [
"https://wenmr.science.uu.nl/conditions"
] ]
}, },
{ {
@ -283,5 +336,10 @@
"field": "consenttermsofusedate", "field": "consenttermsofusedate",
"type": "date", "type": "date",
"value": "2022-03-11" "value": "2022-03-11"
},
{
"field": "lastconsenttermsofusedate",
"type": "date",
"value": "2022-03-11"
} }
] ]

89
dhp-workflows/dhp-graph-provision/src/main/java/eu/dnetlib/dhp/oa/provision/utils/XmlRecordFactory.java
View File

@ -535,6 +535,12 @@ public class XmlRecordFactory implements Serializable {
if (ds.getDatasourcetypeui() != null) { if (ds.getDatasourcetypeui() != null) {
metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", ds.getDatasourcetypeui())); metadata.add(XmlSerializationUtils.mapQualifier("datasourcetypeui", ds.getDatasourcetypeui()));
} }
if (ds.getEosctype() != null) {
metadata.add(XmlSerializationUtils.mapQualifier("eosctype", ds.getEosctype()));
}
if (ds.getEoscdatasourcetype() != null) {
metadata.add(XmlSerializationUtils.mapQualifier("eoscdatasourcetype", ds.getEoscdatasourcetype()));
}
if (ds.getOpenairecompatibility() != null) { if (ds.getOpenairecompatibility() != null) {
metadata metadata
.add( .add(
@ -583,6 +589,16 @@ public class XmlRecordFactory implements Serializable {
metadata metadata
.add(XmlSerializationUtils.asXmlElement("description", ds.getDescription().getValue())); .add(XmlSerializationUtils.asXmlElement("description", ds.getDescription().getValue()));
} }
if (ds.getSubjects() != null) {
metadata
.addAll(
ds
.getSubjects()
.stream()
.filter(Objects::nonNull)
.map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp))
.collect(Collectors.toList()));
}
if (ds.getOdnumberofitems() != null) { if (ds.getOdnumberofitems() != null) {
metadata metadata
.add( .add(
@ -609,6 +625,16 @@ public class XmlRecordFactory implements Serializable {
.map(c -> XmlSerializationUtils.asXmlElement("odlanguages", c.getValue())) .map(c -> XmlSerializationUtils.asXmlElement("odlanguages", c.getValue()))
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
if (ds.getLanguages() != null) {
metadata
.addAll(
ds
.getLanguages()
.stream()
.filter(Objects::nonNull)
.map(c -> XmlSerializationUtils.asXmlElement("languages", c))
.collect(Collectors.toList()));
}
if (ds.getOdcontenttypes() != null) { if (ds.getOdcontenttypes() != null) {
metadata metadata
.addAll( .addAll(
@ -689,18 +715,18 @@ public class XmlRecordFactory implements Serializable {
XmlSerializationUtils XmlSerializationUtils
.asXmlElement("versioning", ds.getVersioning().getValue().toString())); .asXmlElement("versioning", ds.getVersioning().getValue().toString()));
} }
if (ds.getVersioncontrol() != null) {
metadata
.add(
XmlSerializationUtils
.asXmlElement("versioncontrol", ds.getVersioncontrol().toString()));
}
if (ds.getCitationguidelineurl() != null) { if (ds.getCitationguidelineurl() != null) {
metadata metadata
.add( .add(
XmlSerializationUtils XmlSerializationUtils
.asXmlElement("citationguidelineurl", ds.getCitationguidelineurl().getValue())); .asXmlElement("citationguidelineurl", ds.getCitationguidelineurl().getValue()));
} }
if (ds.getQualitymanagementkind() != null) {
metadata
.add(
XmlSerializationUtils
.asXmlElement("qualitymanagementkind", ds.getQualitymanagementkind().getValue()));
}
if (ds.getPidsystems() != null) { if (ds.getPidsystems() != null) {
metadata metadata
.add(XmlSerializationUtils.asXmlElement("pidsystems", ds.getPidsystems().getValue())); .add(XmlSerializationUtils.asXmlElement("pidsystems", ds.getPidsystems().getValue()));
@ -722,17 +748,24 @@ public class XmlRecordFactory implements Serializable {
if (ds.getJournal() != null) { if (ds.getJournal() != null) {
metadata.add(XmlSerializationUtils.mapJournal(ds.getJournal())); metadata.add(XmlSerializationUtils.mapJournal(ds.getJournal()));
} }
if (ds.getSubjects() != null) { if (ds.getResearchentitytypes() != null) {
metadata metadata
.addAll( .addAll(
ds ds
.getSubjects() .getResearchentitytypes()
.stream() .stream()
.filter(Objects::nonNull) .map(c -> XmlSerializationUtils.asXmlElement("researchentitytypes", c))
.map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp)) .collect(Collectors.toList()));
}
if (ds.getProvidedproducttypes() != null) {
metadata
.addAll(
ds
.getProvidedproducttypes()
.stream()
.map(c -> XmlSerializationUtils.asXmlElement("providedproducttypes", c))
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
if (ds.getJurisdiction() != null) { if (ds.getJurisdiction() != null) {
metadata.add(XmlSerializationUtils.mapQualifier("jurisdiction", ds.getJurisdiction())); metadata.add(XmlSerializationUtils.mapQualifier("jurisdiction", ds.getJurisdiction()));
} }
@ -741,11 +774,6 @@ public class XmlRecordFactory implements Serializable {
metadata.add(XmlSerializationUtils.asXmlElement("thematic", ds.getThematic().toString())); metadata.add(XmlSerializationUtils.asXmlElement("thematic", ds.getThematic().toString()));
} }
if (ds.getKnowledgegraph() != null) {
metadata
.add(XmlSerializationUtils.asXmlElement("knowledgegraph", ds.getKnowledgegraph().toString()));
}
if (ds.getContentpolicies() != null) { if (ds.getContentpolicies() != null) {
metadata metadata
.addAll( .addAll(
@ -756,7 +784,34 @@ public class XmlRecordFactory implements Serializable {
.map(q -> XmlSerializationUtils.mapQualifier("contentpolicy", q)) .map(q -> XmlSerializationUtils.mapQualifier("contentpolicy", q))
.collect(Collectors.toList())); .collect(Collectors.toList()));
} }
if (ds.getSubmissionpolicyurl() != null) {
metadata
.add(XmlSerializationUtils.asXmlElement("submissionpolicyurl", ds.getSubmissionpolicyurl()));
}
if (ds.getPreservationpolicyurl() != null) {
metadata
.add(
XmlSerializationUtils.asXmlElement("preservationpolicyurl", ds.getPreservationpolicyurl()));
}
if (ds.getResearchproductaccesspolicies() != null) {
metadata
.addAll(
ds
.getResearchproductaccesspolicies()
.stream()
.map(c -> XmlSerializationUtils.asXmlElement("researchproductaccesspolicies", c))
.collect(Collectors.toList()));
}
if (ds.getResearchproductmetadataaccesspolicies() != null) {
metadata
.addAll(
ds
.getResearchproductmetadataaccesspolicies()
.stream()
.map(
c -> XmlSerializationUtils.asXmlElement("researchproductmetadataaccesspolicies", c))
.collect(Collectors.toList()));
}
break; break;
case organization: case organization:
final Organization o = (Organization) entity; final Organization o = (Organization) entity;

11
dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java
View File

@ -11,6 +11,7 @@ import java.util.List;
import org.apache.commons.io.IOUtils; import org.apache.commons.io.IOUtils;
import org.dom4j.Document; import org.dom4j.Document;
import org.dom4j.DocumentException; import org.dom4j.DocumentException;
import org.dom4j.Element;
import org.dom4j.io.SAXReader; import org.dom4j.io.SAXReader;
import org.junit.jupiter.api.Test; import org.junit.jupiter.api.Test;
@ -142,7 +143,7 @@ public class XmlRecordFactoryTest {
} }
@Test @Test
public void testDatasource() throws IOException, DocumentException { public void testService() throws IOException, DocumentException {
final ContextMapper contextMapper = new ContextMapper(); final ContextMapper contextMapper = new ContextMapper();
final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false,
@ -167,6 +168,14 @@ public class XmlRecordFactoryTest {
assertEquals("true", doc.valueOf("//thematic")); assertEquals("true", doc.valueOf("//thematic"));
assertEquals("Journal article", doc.valueOf("//contentpolicy/@classname")); assertEquals("Journal article", doc.valueOf("//contentpolicy/@classname"));
assertEquals("Journal archive", doc.valueOf("//datasourcetypeui/@classname")); assertEquals("Journal archive", doc.valueOf("//datasourcetypeui/@classname"));
assertEquals("Data Source", doc.valueOf("//eosctype/@classname"));
final List pids = doc.selectNodes("//pid");
assertEquals(1, pids.size());
assertEquals("re3data", ((Element) pids.get(0)).attribute("classid").getValue());
assertEquals(
"Registry of research data repositories", ((Element) pids.get(0)).attribute("classname").getValue());
assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemeid").getValue());
assertEquals("dnet:pid_types", ((Element) pids.get(0)).attribute("schemename").getValue());
} }
} }

389
dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json
View File

File diff suppressed because one or more lines are too long

2
pom.xml
View File

@ -801,7 +801,7 @@
<mockito-core.version>3.3.3</mockito-core.version> <mockito-core.version>3.3.3</mockito-core.version>
<mongodb.driver.version>3.4.2</mongodb.driver.version> <mongodb.driver.version>3.4.2</mongodb.driver.version>
<vtd.version>[2.12,3.0)</vtd.version> <vtd.version>[2.12,3.0)</vtd.version>
<dhp-schemas.version>[2.10.32]</dhp-schemas.version> <dhp-schemas.version>[2.12.0]</dhp-schemas.version>
<dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version> <dnet-actionmanager-api.version>[4.0.3]</dnet-actionmanager-api.version>
<dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version> <dnet-actionmanager-common.version>[6.0.5]</dnet-actionmanager-common.version>
<dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version> <dnet-openaire-broker-common.version>[3.1.6]</dnet-openaire-broker-common.version>