diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java b/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java index 91c6c1825..fac9a7565 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/common/PacePerson.java @@ -1,18 +1,18 @@ package eu.dnetlib.dhp.common; +import java.io.IOException; import java.nio.charset.StandardCharsets; import java.text.Normalizer; -import java.util.HashSet; -import java.util.List; -import java.util.Set; +import java.util.*; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.text.WordUtils; +import com.ctc.wstx.dtd.LargePrefixedNameSet; import com.google.common.base.Joiner; import com.google.common.base.Splitter; -import com.google.common.collect.Iterables; import com.google.common.collect.Lists; import com.google.common.hash.Hashing; @@ -29,7 +29,19 @@ public class PacePerson { private List fullname = Lists.newArrayList(); private final String original; - private static Set particles = null; + private static Set particles; + + static { + try { + particles = new HashSet<>(IOUtils + .readLines( + PacePerson.class + .getResourceAsStream( + "/eu/dnetlib/dhp/common/name_particles.txt"))); + } catch (IOException e) { + throw new RuntimeException(e); + } + } /** * Capitalizes a string @@ -37,29 +49,20 @@ public class PacePerson { * @param s the string to capitalize * @return the input string with capital letter */ - public static final String capitalize(final String s) { + public static String capitalize(final String s) { + if (particles.contains(s)) { + return s; + } return WordUtils.capitalize(s.toLowerCase(), ' ', '-'); } /** * Adds a dot to a string with length equals to 1 */ - public static final String dotAbbreviations(final String s) { + public static String dotAbbreviations(final String s) { return s.length() == 1 ? s + "." : s; } - public static Set loadFromClasspath(final String classpath) { - final Set h = new HashSet<>(); - try { - for (final String s : IOUtils.readLines(PacePerson.class.getResourceAsStream(classpath))) { - h.add(s); - } - } catch (final Throwable e) { - return new HashSet<>(); - } - return h; - } - /** * The constructor of the class. It fills the fields of the class basing on the input fullname. * @@ -128,10 +131,6 @@ public class PacePerson { } private List splitTerms(final String s) { - if (particles == null) { - particles = loadFromClasspath("/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt"); - } - final List list = Lists.newArrayList(); for (final String part : Splitter.on(" ").omitEmptyStrings().split(s)) { if (!particles.contains(part.toLowerCase())) { @@ -187,17 +186,36 @@ public class PacePerson { } public List getCapitalFirstnames() { - return Lists - .newArrayList( - Iterables.transform(getNameWithAbbreviations(), PacePerson::capitalize)); + return Optional + .ofNullable(getNameWithAbbreviations()) + .map( + name -> name + .stream() + .map(PacePerson::capitalize) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); } public List getCapitalSurname() { - return Lists.newArrayList(Iterables.transform(surname, PacePerson::capitalize)); + return Optional + .ofNullable(getSurname()) + .map( + surname -> surname + .stream() + .map(PacePerson::capitalize) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); } public List getNameWithAbbreviations() { - return Lists.newArrayList(Iterables.transform(name, PacePerson::dotAbbreviations)); + return Optional + .ofNullable(getName()) + .map( + name -> name + .stream() + .map(PacePerson::dotAbbreviations) + .collect(Collectors.toList())) + .orElse(new ArrayList<>()); } public boolean isAccurate() { diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java index 0a51e8600..ac9cfe330 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtils.java @@ -3,6 +3,8 @@ package eu.dnetlib.dhp.schema.oaf.utils; import static eu.dnetlib.dhp.schema.common.ModelConstants.*; +import java.sql.Array; +import java.sql.SQLException; import java.util.*; import java.util.concurrent.ConcurrentHashMap; import java.util.function.Function; @@ -118,6 +120,17 @@ public class OafMapperUtils { .collect(Collectors.toList()); } + public static List 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> listFields(final DataInfo info, final List values) { return values .stream() @@ -391,4 +404,19 @@ public class OafMapperUtils { } return null; } + + public static KeyValue newKeyValueInstance(String key, String value, DataInfo dataInfo) { + KeyValue kv = new KeyValue(); + kv.setDataInfo(dataInfo); + kv.setKey(key); + kv.setValue(value); + return kv; + } + + public static Measure newMeasureInstance(String id, String value, String key, DataInfo dataInfo) { + Measure m = new Measure(); + m.setId(id); + m.setUnit(Arrays.asList(newKeyValueInstance(key, value, dataInfo))); + return m; + } } diff --git a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java index 5a59bc0df..e10d0c500 100644 --- a/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java +++ b/dhp-common/src/main/java/eu/dnetlib/dhp/utils/DHPUtils.java @@ -75,9 +75,14 @@ public class DHPUtils { final HttpGet req = new HttpGet(url); + log.info("MDStoreManager request: {}", req); + try (final CloseableHttpClient client = HttpClients.createDefault()) { try (final CloseableHttpResponse response = client.execute(req)) { final String json = IOUtils.toString(response.getEntity().getContent()); + + log.info("MDStoreManager response: {}", json); + final MDStoreWithInfo[] mdstores = objectMapper.readValue(json, MDStoreWithInfo[].class); return Arrays .stream(mdstores) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt b/dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt similarity index 76% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt rename to dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt index dae37c9dc..07cf06a98 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/pace/name_particles.txt +++ b/dhp-common/src/main/resources/eu/dnetlib/dhp/common/name_particles.txt @@ -1,7 +1,8 @@ van +von der de dell sig mr -mrs +mrs \ No newline at end of file diff --git a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java index 79629a171..9111ac2df 100644 --- a/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java +++ b/dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/OafMapperUtilsTest.java @@ -44,105 +44,104 @@ class OafMapperUtilsTest { @Test void testDateValidation() { - assertTrue(GraphCleaningFunctions.doCleanDate("2016-05-07T12:41:19.202Z ").isPresent()); - assertTrue(GraphCleaningFunctions.doCleanDate("2020-09-10 11:08:52 ").isPresent()); - assertTrue(GraphCleaningFunctions.doCleanDate(" 2016-04-05").isPresent()); + assertNotNull(GraphCleaningFunctions.cleanDate("2016-05-07T12:41:19.202Z ")); + assertNotNull(GraphCleaningFunctions.cleanDate("2020-09-10 11:08:52 ")); + 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("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct 7, '70").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("oct. 7, 70").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 2 15:04:05 MST 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon Jan 02 15:04:05 -0700 2006").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Monday, 02-Jan-06 15:04:05 MST").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 MST").get()); - assertEquals("2017-07-11", GraphCleaningFunctions.doCleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("Mon, 02 Jan 2006 15:04:05 -0700").get()); - assertEquals("2018-01-04", GraphCleaningFunctions.doCleanDate("Thu, 4 Jan 2018 17:53:36 +0000").get()); - assertEquals("2015-08-10", GraphCleaningFunctions.doCleanDate("Mon Aug 10 15:44:11 UTC+0100 2015").get()); + assertEquals("2009-05-08", GraphCleaningFunctions.cleanDate("May 8, 2009 5:57:51 PM")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct 7, '70")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("oct. 7, 70")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 2 15:04:05 MST 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon Jan 02 15:04:05 -0700 2006")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Monday, 02-Jan-06 15:04:05 MST")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 MST")); + assertEquals("2017-07-11", GraphCleaningFunctions.cleanDate("Tue, 11 Jul 2017 16:28:13 +0200 (CEST)")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("Mon, 02 Jan 2006 15:04:05 -0700")); + assertEquals("2018-01-04", GraphCleaningFunctions.cleanDate("Thu, 4 Jan 2018 17:53:36 +0000")); + assertEquals("2015-08-10", GraphCleaningFunctions.cleanDate("Mon Aug 10 15:44:11 UTC+0100 2015")); assertEquals( "2015-07-03", - GraphCleaningFunctions.doCleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 10:09am").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012 at 10:09am PST-08").get()); - assertEquals("2012-09-17", GraphCleaningFunctions.doCleanDate("September 17, 2012, 10:10:09").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7, 1970").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("October 7th, 1970").get()); - assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006, 19:17").get()); - assertEquals("2006-02-12", GraphCleaningFunctions.doCleanDate("12 Feb 2006 19:17").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 70").get()); - assertEquals("1970-10-07", GraphCleaningFunctions.doCleanDate("7 oct 1970").get()); - assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("03 February 2013").get()); - assertEquals("2013-07-01", GraphCleaningFunctions.doCleanDate("1 July 2013").get()); - assertEquals("2013-02-03", GraphCleaningFunctions.doCleanDate("2013-Feb-03").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3/31/2014").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03/31/2014").get()); - assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08/21/71").get()); - assertEquals("1971-01-08", GraphCleaningFunctions.doCleanDate("8/1/71").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/2014 22:05").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("04/08/2014 22:05").get()); - assertEquals("2014-08-04", GraphCleaningFunctions.doCleanDate("4/8/14 22:05").get()); - assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("04/2/2014 03:00:51").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00:00 AM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00:01 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 01:00 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 1:00 PM").get()); - assertEquals("1965-08-08", GraphCleaningFunctions.doCleanDate("8/8/1965 12:00 AM").get()); - assertEquals("2014-02-04", GraphCleaningFunctions.doCleanDate("4/02/2014 03:00:51").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("03/19/2012 10:11:59.3186369").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/3/31").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("2014/03/31").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/4/8 22:05").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014/04/08 22:05").get()); - assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/04/2 03:00:51").get()); - assertEquals("2014-04-02", GraphCleaningFunctions.doCleanDate("2014/4/02 03:00:51").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("2012/03/19 10:11:59.3186369").get()); - assertEquals("2014-04-08", GraphCleaningFunctions.doCleanDate("2014年04月08日").get()); - assertEquals("2006-01-02", GraphCleaningFunctions.doCleanDate("2006-01-02T15:04:05+0000").get()); - assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09-07:00").get()); - assertEquals("2009-08-12", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09").get()); - assertEquals("2009-08-13", GraphCleaningFunctions.doCleanDate("2009-08-12T22:15:09Z").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.3186369").get()); - assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 17:24:37.123").get()); - assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43").get()); - assertEquals("2013-04-01", GraphCleaningFunctions.doCleanDate("2013-04-01 22:43:22").get()); - assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 UTC").get()); - assertEquals("2014-12-16", GraphCleaningFunctions.doCleanDate("2014-12-16 06:20:00 GMT").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 05:24:37 PM").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:43 +0800 +08").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26 13:13:44 +09:00").get()); - assertEquals("2012-08-03", GraphCleaningFunctions.doCleanDate("2012-08-03 18:31:59.257000000 +0000 UTC").get()); - assertEquals("2015-09-30", GraphCleaningFunctions.doCleanDate("2015-09-30 18:48:56.35272715 +0000 UTC").get()); - assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 GMT").get()); - assertEquals("2015-02-18", GraphCleaningFunctions.doCleanDate("2015-02-18 00:12:00 +0000 UTC").get()); + GraphCleaningFunctions.cleanDate("Fri Jul 03 2015 18:04:07 GMT+0100 (GMT Daylight Time)")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 10:09am")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012 at 10:09am PST-08")); + assertEquals("2012-09-17", GraphCleaningFunctions.cleanDate("September 17, 2012, 10:10:09")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7, 1970")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("October 7th, 1970")); + assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006, 19:17")); + assertEquals("2006-02-12", GraphCleaningFunctions.cleanDate("12 Feb 2006 19:17")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 70")); + assertEquals("1970-10-07", GraphCleaningFunctions.cleanDate("7 oct 1970")); + assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("03 February 2013")); + assertEquals("2013-07-01", GraphCleaningFunctions.cleanDate("1 July 2013")); + assertEquals("2013-02-03", GraphCleaningFunctions.cleanDate("2013-Feb-03")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3/31/2014")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03/31/2014")); + assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08/21/71")); + assertEquals("1971-01-08", GraphCleaningFunctions.cleanDate("8/1/71")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/2014 22:05")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("04/08/2014 22:05")); + assertEquals("2014-08-04", GraphCleaningFunctions.cleanDate("4/8/14 22:05")); + assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("04/2/2014 03:00:51")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00:00 AM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00:01 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 01:00 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 1:00 PM")); + assertEquals("1965-08-08", GraphCleaningFunctions.cleanDate("8/8/1965 12:00 AM")); + assertEquals("2014-02-04", GraphCleaningFunctions.cleanDate("4/02/2014 03:00:51")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("03/19/2012 10:11:59.3186369")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/3/31")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("2014/03/31")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/4/8 22:05")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014/04/08 22:05")); + assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/04/2 03:00:51")); + assertEquals("2014-04-02", GraphCleaningFunctions.cleanDate("2014/4/02 03:00:51")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("2012/03/19 10:11:59.3186369")); + assertEquals("2014-04-08", GraphCleaningFunctions.cleanDate("2014年04月08日")); + assertEquals("2006-01-02", GraphCleaningFunctions.cleanDate("2006-01-02T15:04:05+0000")); + assertEquals("2009-08-13", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09-07:00")); + assertEquals("2009-08-12", GraphCleaningFunctions.cleanDate("2009-08-12T22:15:09")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.3186369")); + assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 17:24:37.123")); + assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43")); + assertEquals("2013-04-01", GraphCleaningFunctions.cleanDate("2013-04-01 22:43:22")); + assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 UTC")); + assertEquals("2014-12-16", GraphCleaningFunctions.cleanDate("2014-12-16 06:20:00 GMT")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 05:24:37 PM")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:43 +0800 +08")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26 13:13:44 +09:00")); + assertEquals("2012-08-03", GraphCleaningFunctions.cleanDate("2012-08-03 18:31:59.257000000 +0000 UTC")); + assertEquals("2015-09-30", GraphCleaningFunctions.cleanDate("2015-09-30 18:48:56.35272715 +0000 UTC")); + assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 GMT")); + assertEquals("2015-02-18", GraphCleaningFunctions.cleanDate("2015-02-18 00:12:00 +0000 UTC")); 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( - "2015-02-08", GraphCleaningFunctions.doCleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001").get()); - assertEquals("2017-07-19", GraphCleaningFunctions.doCleanDate("2017-07-19 03:21:51+00:00").get()); - assertEquals("2014-04-26", GraphCleaningFunctions.doCleanDate("2014-04-26").get()); - assertEquals("2014-04-01", GraphCleaningFunctions.doCleanDate("2014-04").get()); - assertEquals("2014-01-01", GraphCleaningFunctions.doCleanDate("2014").get()); - assertEquals("2014-05-11", GraphCleaningFunctions.doCleanDate("2014-05-11 08:20:13,787").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("3.31.2014").get()); - assertEquals("2014-03-31", GraphCleaningFunctions.doCleanDate("03.31.2014").get()); - assertEquals("1971-08-21", GraphCleaningFunctions.doCleanDate("08.21.71").get()); - assertEquals("2014-03-01", GraphCleaningFunctions.doCleanDate("2014.03").get()); - assertEquals("2014-03-30", GraphCleaningFunctions.doCleanDate("2014.03.30").get()); - assertEquals("2014-06-01", GraphCleaningFunctions.doCleanDate("20140601").get()); - assertEquals("2014-07-22", GraphCleaningFunctions.doCleanDate("20140722105203").get()); - assertEquals("2012-03-19", GraphCleaningFunctions.doCleanDate("1332151919").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367189").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222").get()); - assertEquals("2013-11-12", GraphCleaningFunctions.doCleanDate("1384216367111222333").get()); + "2015-02-08", GraphCleaningFunctions.cleanDate("2015-02-08 03:02:00.001 +0300 MSK m=+0.000000001")); + assertEquals("2017-07-19", GraphCleaningFunctions.cleanDate("2017-07-19 03:21:51+00:00")); + assertEquals("2014-04-26", GraphCleaningFunctions.cleanDate("2014-04-26")); + assertEquals("2014-04-01", GraphCleaningFunctions.cleanDate("2014-04")); + assertEquals("2014-01-01", GraphCleaningFunctions.cleanDate("2014")); + assertEquals("2014-05-11", GraphCleaningFunctions.cleanDate("2014-05-11 08:20:13,787")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("3.31.2014")); + assertEquals("2014-03-31", GraphCleaningFunctions.cleanDate("03.31.2014")); + assertEquals("1971-08-21", GraphCleaningFunctions.cleanDate("08.21.71")); + assertEquals("2014-03-01", GraphCleaningFunctions.cleanDate("2014.03")); + assertEquals("2014-03-30", GraphCleaningFunctions.cleanDate("2014.03.30")); + assertEquals("2014-06-01", GraphCleaningFunctions.cleanDate("20140601")); + assertEquals("2014-07-22", GraphCleaningFunctions.cleanDate("20140722105203")); + assertEquals("2012-03-19", GraphCleaningFunctions.cleanDate("1332151919")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367189")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222")); + assertEquals("2013-11-12", GraphCleaningFunctions.cleanDate("1384216367111222333")); } diff --git a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java index 99ce961aa..df9202ed8 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java +++ b/dhp-workflows/dhp-actionmanager/src/test/java/eu/dnetlib/dhp/actionmanager/promote/PromoteActionPayloadForGraphTableJobTest.java @@ -172,6 +172,61 @@ public class PromoteActionPayloadForGraphTableJobTest { } } + @Test + void shouldPromoteActionPayload_custom() throws Exception { + + Class rowClazz = Publication.class; + Class actionPayloadClazz = Result.class; + MergeAndGet.Strategy strategy = MergeAndGet.Strategy.MERGE_FROM_AND_GET; + + // given + Path inputGraphTableDir = createGraphTable(inputGraphRootDir, rowClazz); + Path inputActionPayloadDir = createActionPayload(inputActionPayloadRootDir, rowClazz, actionPayloadClazz); + Path outputGraphTableDir = outputDir.resolve("graph").resolve(rowClazz.getSimpleName().toLowerCase()); + + // when + PromoteActionPayloadForGraphTableJob + .main( + new String[] { + "-isSparkSessionManaged", + Boolean.FALSE.toString(), + "-inputGraphTablePath", + inputGraphTableDir.toString(), + "-graphTableClassName", + rowClazz.getCanonicalName(), + "-inputActionPayloadPath", + inputActionPayloadDir.toString(), + "-actionPayloadClassName", + actionPayloadClazz.getCanonicalName(), + "-outputGraphTablePath", + outputGraphTableDir.toString(), + "-mergeAndGetStrategy", + strategy.name(), + "--shouldGroupById", + "true" + }); + + // then + assertTrue(Files.exists(outputGraphTableDir)); + + List actualOutputRows = readGraphTableFromJobOutput(outputGraphTableDir.toString(), rowClazz) + .collectAsList() + .stream() + .sorted(Comparator.comparingInt(Object::hashCode)) + .collect(Collectors.toList()); + + Publication p = actualOutputRows + .stream() + .map(o -> (Publication) o) + .filter(o -> "50|4ScienceCRIS::6a67ed3daba1c380bf9de3c13ed9c879".equals(o.getId())) + .findFirst() + .get(); + + assertNotNull(p.getMeasures()); + assertTrue(p.getMeasures().size() > 0); + + } + public static Stream promoteJobTestParams() { return Stream .of( diff --git a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json index f98ee4b78..d98bfe98f 100644 --- a/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json +++ b/dhp-workflows/dhp-actionmanager/src/test/resources/eu/dnetlib/dhp/actionmanager/promote/input/action_payload/publication_table/result.json @@ -17,4 +17,5 @@ {"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"","inferenceprovenance":"","provenanceaction":{"classid":"","classname":"","schemeid":"","schemename":""}},"lastupdatetimestamp":1572018243405,"id":"50|CSC_________::00019460865d6cc381b36076131a5bc1","originalId":[],"collectedfrom":[],"pid":[],"dateofcollection":"","dateoftransformation":"","extraInfo":[],"oaiprovenance":null,"author":[],"resulttype":{"classid":"","classname":"","schemeid":"","schemename":""},"language":{"classid":"","classname":"","schemeid":"","schemename":""},"country":[],"subject":[{"value":"Computer Science::Networking and Internet 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"Inferred by OpenAIRE"; public static final String UPDATE_MEASURE_BIP_CLASS_ID = "measure:bip"; public static final String UPDATE_SUBJECT_SDG_CLASS_ID = "subject:sdg"; + public static final String UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID = "measure:usage_counts"; + public static final String UPDATE_KEY_USAGE_COUNTS = "count"; public static final String FOS_CLASS_ID = "FOS"; public static final String FOS_CLASS_NAME = "Fields of Science and Technology classification"; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java new file mode 100644 index 000000000..5f099b8f2 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionUsageJob.java @@ -0,0 +1,156 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import static eu.dnetlib.dhp.actionmanager.Constants.*; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkHiveSession; + +import java.io.Serializable; +import java.util.Arrays; +import java.util.List; +import java.util.Optional; + +import org.apache.commons.io.IOUtils; +import org.apache.hadoop.io.Text; +import org.apache.hadoop.mapred.SequenceFileOutputFormat; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.api.java.function.MapGroupsFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.DataInfo; +import eu.dnetlib.dhp.schema.oaf.Measure; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; +import scala.Tuple2; + +/** + * created the Atomic Action for each type of results + */ +public class SparkAtomicActionUsageJob implements Serializable { + + private static final Logger log = LoggerFactory.getLogger(SparkAtomicActionUsageJob.class); + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + SparkAtomicActionUsageJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String outputPath = parser.get("outputPath"); + log.info("outputPath {}: ", outputPath); + + SparkConf conf = new SparkConf(); + conf.set("hive.metastore.uris", parser.get("hive_metastore_uris")); + + final String dbname = parser.get("usagestatsdb"); + + final String workingPath = parser.get("workingPath"); + + runWithSparkHiveSession( + conf, + isSparkSessionManaged, + spark -> { + removeOutputDir(spark, outputPath); + prepareResults(dbname, spark, workingPath); + writeActionSet(spark, workingPath, outputPath); + }); + } + + public static void prepareResults(String db, SparkSession spark, String workingPath) { + spark + .sql( + "Select result_id, downloads, views " + + "from " + db + ".usage_stats") + .as(Encoders.bean(UsageStatsModel.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); + } + + public static void writeActionSet(SparkSession spark, String inputPath, String outputPath) { + readPath(spark, inputPath, UsageStatsModel.class) + .groupByKey((MapFunction) us -> us.getResult_id(), Encoders.STRING()) + .mapGroups((MapGroupsFunction) (k, it) -> { + UsageStatsModel first = it.next(); + it.forEachRemaining(us -> { + first.setDownloads(first.getDownloads() + us.getDownloads()); + first.setViews(first.getViews() + us.getViews()); + }); + + Result res = new Result(); + res.setId("50|" + k); + + res.setMeasures(getMeasure(first.getDownloads(), first.getViews())); + return res; + }, Encoders.bean(Result.class)) + .toJavaRDD() + .map(p -> new AtomicAction(p.getClass(), p)) + .mapToPair( + aa -> new Tuple2<>(new Text(aa.getClazz().getCanonicalName()), + new Text(OBJECT_MAPPER.writeValueAsString(aa)))) + .saveAsHadoopFile(outputPath, Text.class, Text.class, SequenceFileOutputFormat.class); + + } + + private static List getMeasure(Long downloads, Long views) { + DataInfo dataInfo = OafMapperUtils + .dataInfo( + false, + UPDATE_DATA_INFO_TYPE, + true, + false, + OafMapperUtils + .qualifier( + UPDATE_MEASURE_USAGE_COUNTS_CLASS_ID, + UPDATE_CLASS_NAME, + ModelConstants.DNET_PROVENANCE_ACTIONS, + ModelConstants.DNET_PROVENANCE_ACTIONS), + ""); + + return Arrays + .asList( + OafMapperUtils + .newMeasureInstance("downloads", String.valueOf(downloads), UPDATE_KEY_USAGE_COUNTS, dataInfo), + OafMapperUtils.newMeasureInstance("views", String.valueOf(views), UPDATE_KEY_USAGE_COUNTS, dataInfo)); + + } + + private static void removeOutputDir(SparkSession spark, String path) { + HdfsSupport.remove(path, spark.sparkContext().hadoopConfiguration()); + } + + public static Dataset readPath( + SparkSession spark, String inputPath, Class clazz) { + return spark + .read() + .textFile(inputPath) + .map((MapFunction) value -> OBJECT_MAPPER.readValue(value, clazz), Encoders.bean(clazz)); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java new file mode 100644 index 000000000..df8a77eb6 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/actionmanager/usagestats/UsageStatsModel.java @@ -0,0 +1,34 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import java.io.Serializable; + +public class UsageStatsModel implements Serializable { + private String result_id; + private Long downloads; + private Long views; + + public String getResult_id() { + return result_id; + } + + public void setResult_id(String result_id) { + this.result_id = result_id; + } + + public Long getDownloads() { + return downloads; + } + + public void setDownloads(Long downloads) { + this.downloads = downloads; + } + + public Long getViews() { + return views; + } + + public void setViews(Long views) { + this.views = views; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java index 2ea3f35cc..9d9400068 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/CollectorWorker.java @@ -19,6 +19,8 @@ import org.slf4j.LoggerFactory; import eu.dnetlib.dhp.aggregation.common.ReporterCallback; import eu.dnetlib.dhp.aggregation.common.ReportingJob; import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.file.FileCollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.file.FileGZipCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.mongodb.MDStoreCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.mongodb.MongoDbDumpCollectorPlugin; import eu.dnetlib.dhp.collection.plugin.oai.OaiCollectorPlugin; @@ -114,6 +116,10 @@ public class CollectorWorker extends ReportingJob { return new OaiCollectorPlugin(clientParams); case rest_json2xml: return new RestCollectorPlugin(clientParams); + case file: + return new FileCollectorPlugin(fileSystem); + case fileGZip: + return new FileGZipCollectorPlugin(fileSystem); case other: final CollectorPlugin.NAME.OTHER_NAME plugin = Optional .ofNullable(api.getParams().get("other_plugin_type")) diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java index 841d42fea..08084e22a 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/CollectorPlugin.java @@ -10,7 +10,7 @@ import eu.dnetlib.dhp.common.collection.CollectorException; public interface CollectorPlugin { enum NAME { - oai, other, rest_json2xml; + oai, other, rest_json2xml, file, fileGZip; public enum OTHER_NAME { mdstore_mongodb_dump, mdstore_mongodb diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java new file mode 100644 index 000000000..f2fa3d2bb --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/AbstractSplittedRecordPlugin.java @@ -0,0 +1,80 @@ + +package eu.dnetlib.dhp.collection.plugin.file; + +import java.io.BufferedInputStream; +import java.io.IOException; +import java.util.Iterator; +import java.util.Optional; +import java.util.Spliterator; +import java.util.Spliterators; +import java.util.stream.Stream; +import java.util.stream.StreamSupport; + +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.collection.plugin.CollectorPlugin; +import eu.dnetlib.dhp.collection.plugin.utils.XMLIterator; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; + +public abstract class AbstractSplittedRecordPlugin implements CollectorPlugin { + + private static final Logger log = LoggerFactory.getLogger(AbstractSplittedRecordPlugin.class); + + public static final String SPLIT_ON_ELEMENT = "splitOnElement"; + + private final FileSystem fileSystem; + + public AbstractSplittedRecordPlugin(FileSystem fileSystem) { + this.fileSystem = fileSystem; + } + + @Override + public Stream collect(ApiDescriptor api, AggregatorReport report) throws CollectorException { + + // get path to file + final Path filePath = Optional + .ofNullable(api.getBaseUrl()) + .map(Path::new) + .orElseThrow(() -> new CollectorException("missing baseUrl")); + + log.info("baseUrl: {}", filePath); + + // check that path to file exists + try { + if (!fileSystem.exists(filePath)) { + throw new CollectorException("path does not exist: " + filePath); + } + } catch (IOException e) { + throw new CollectorException(e); + } + + // get split element + final String splitOnElement = Optional + .ofNullable(api.getParams().get(SPLIT_ON_ELEMENT)) + .orElseThrow( + () -> new CollectorException(String + .format("missing parameter '%s', required by the AbstractSplittedRecordPlugin", SPLIT_ON_ELEMENT))); + + log.info("splitOnElement: {}", splitOnElement); + + final BufferedInputStream bis = getBufferedInputStream(filePath); + + Iterator xmlIterator = new XMLIterator(splitOnElement, bis); + + return StreamSupport + .stream( + Spliterators.spliteratorUnknownSize(xmlIterator, Spliterator.ORDERED), + false); + } + + abstract protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException; + + public FileSystem getFileSystem() { + return fileSystem; + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java new file mode 100644 index 000000000..f771def93 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPlugin.java @@ -0,0 +1,33 @@ + +package eu.dnetlib.dhp.collection.plugin.file; + +import java.io.BufferedInputStream; + +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.common.collection.CollectorException; + +public class FileCollectorPlugin extends AbstractSplittedRecordPlugin { + + private static final Logger log = LoggerFactory.getLogger(FileCollectorPlugin.class); + + public FileCollectorPlugin(FileSystem fileSystem) { + super(fileSystem); + } + + @Override + protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException { + + log.info("filePath: {}", filePath); + + try { + FileSystem fs = super.getFileSystem(); + return new BufferedInputStream(fs.open(filePath)); + } catch (Exception e) { + throw new CollectorException("Error reading file " + filePath, e); + } + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java new file mode 100644 index 000000000..91a6e9f16 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPlugin.java @@ -0,0 +1,35 @@ + +package eu.dnetlib.dhp.collection.plugin.file; + +import java.io.BufferedInputStream; +import java.util.zip.GZIPInputStream; + +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.Path; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.common.collection.CollectorException; + +public class FileGZipCollectorPlugin extends AbstractSplittedRecordPlugin { + + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPlugin.class); + + public FileGZipCollectorPlugin(FileSystem fileSystem) { + super(fileSystem); + } + + @Override + protected BufferedInputStream getBufferedInputStream(final Path filePath) throws CollectorException { + + log.info("filePath: {}", filePath); + + try { + FileSystem fs = super.getFileSystem(); + GZIPInputStream stream = new GZIPInputStream(fs.open(filePath)); + return new BufferedInputStream(stream); + } catch (Exception e) { + throw new CollectorException("Error reading file " + filePath, e); + } + } +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java index 566c6b216..28b2572fb 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/oai/OaiIterator.java @@ -19,7 +19,7 @@ import org.dom4j.io.XMLWriter; import org.slf4j.Logger; import org.slf4j.LoggerFactory; -import eu.dnetlib.dhp.collection.XmlCleaner; +import eu.dnetlib.dhp.collection.plugin.utils.XmlCleaner; import eu.dnetlib.dhp.common.aggregation.AggregatorReport; import eu.dnetlib.dhp.common.collection.CollectorException; import eu.dnetlib.dhp.common.collection.HttpConnector2; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java index 64a041fd4..e4bad2f8d 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/rest/RestIterator.java @@ -30,7 +30,7 @@ import org.w3c.dom.Node; import org.w3c.dom.NodeList; import org.xml.sax.InputSource; -import eu.dnetlib.dhp.collection.JsonUtils; +import eu.dnetlib.dhp.collection.plugin.utils.JsonUtils; import eu.dnetlib.dhp.common.collection.CollectorException; import eu.dnetlib.dhp.common.collection.HttpClientParams; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/JsonUtils.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java similarity index 98% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/JsonUtils.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java index da3768a4a..15401e223 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/JsonUtils.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/JsonUtils.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.collection; +package eu.dnetlib.dhp.collection.plugin.utils; import org.apache.commons.logging.Log; import org.apache.commons.logging.LogFactory; diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java new file mode 100644 index 000000000..e05fe263a --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XMLIterator.java @@ -0,0 +1,177 @@ + +package eu.dnetlib.dhp.collection.plugin.utils; + +import java.io.InputStream; +import java.io.InputStreamReader; +import java.io.Reader; +import java.io.StringWriter; +import java.nio.charset.Charset; +import java.nio.charset.CharsetDecoder; +import java.nio.charset.CodingErrorAction; +import java.util.Iterator; + +import javax.xml.stream.XMLEventFactory; +import javax.xml.stream.XMLEventReader; +import javax.xml.stream.XMLEventWriter; +import javax.xml.stream.XMLInputFactory; +import javax.xml.stream.XMLOutputFactory; +import javax.xml.stream.XMLStreamException; +import javax.xml.stream.events.StartElement; +import javax.xml.stream.events.XMLEvent; + +import org.apache.commons.logging.Log; +import org.apache.commons.logging.LogFactory; + +public class XMLIterator implements Iterator { + + private static final Log log = LogFactory.getLog(XMLIterator.class); + + private ThreadLocal inputFactory = new ThreadLocal() { + + @Override + protected XMLInputFactory initialValue() { + return XMLInputFactory.newInstance(); + } + }; + + private ThreadLocal outputFactory = new ThreadLocal() { + + @Override + protected XMLOutputFactory initialValue() { + return XMLOutputFactory.newInstance(); + } + }; + + private ThreadLocal eventFactory = new ThreadLocal() { + + @Override + protected XMLEventFactory initialValue() { + return XMLEventFactory.newInstance(); + } + }; + + public static final String UTF_8 = "UTF-8"; + + final XMLEventReader parser; + + private XMLEvent current = null; + + private String element; + + private InputStream inputStream; + + public XMLIterator(final String element, final InputStream inputStream) { + super(); + this.element = element; + this.inputStream = inputStream; + this.parser = getParser(); + try { + this.current = findElement(parser); + } catch (XMLStreamException e) { + log.warn("cannot init parser position. No element found: " + element); + current = null; + } + } + + @Override + public boolean hasNext() { + return current != null; + } + + @Override + public String next() { + String result = null; + try { + result = copy(parser); + current = findElement(parser); + return result; + } catch (XMLStreamException e) { + throw new RuntimeException(String.format("error copying xml, built so far: '%s'", result), e); + } + } + + @Override + public void remove() { + throw new UnsupportedOperationException(); + } + + @SuppressWarnings("finally") + private String copy(final XMLEventReader parser) throws XMLStreamException { + final StringWriter result = new StringWriter(); + try { + final XMLEventWriter writer = outputFactory.get().createXMLEventWriter(result); + final StartElement start = current.asStartElement(); + final StartElement newRecord = eventFactory + .get() + .createStartElement(start.getName(), start.getAttributes(), start.getNamespaces()); + + // new root record + writer.add(newRecord); + + // copy the rest as it is + while (parser.hasNext()) { + final XMLEvent event = parser.nextEvent(); + + // TODO: replace with depth tracking instead of close tag tracking. + if (event.isEndElement() && event.asEndElement().getName().getLocalPart().equals(element)) { + writer.add(event); + break; + } + + writer.add(event); + } + writer.close(); + } finally { + return result.toString(); + } + } + + /** + * Looks for the next occurrence of the splitter element. + * + * @param parser + * @return + * @throws XMLStreamException + */ + private XMLEvent findElement(final XMLEventReader parser) throws XMLStreamException { + + /* + * if (current != null && element.equals(current.asStartElement().getName().getLocalPart())) { return current; } + */ + + XMLEvent peek = parser.peek(); + if (peek != null && peek.isStartElement()) { + String name = peek.asStartElement().getName().getLocalPart(); + if (element.equals(name)) { + return peek; + } + } + + while (parser.hasNext()) { + final XMLEvent event = parser.nextEvent(); + if (event != null && event.isStartElement()) { + String name = event.asStartElement().getName().getLocalPart(); + if (element.equals(name)) { + return event; + } + } + } + return null; + } + + private XMLEventReader getParser() { + try { + return inputFactory.get().createXMLEventReader(sanitize(inputStream)); + } catch (XMLStreamException e) { + throw new RuntimeException(e); + } + } + + private Reader sanitize(final InputStream in) { + final CharsetDecoder charsetDecoder = Charset.forName(UTF_8).newDecoder(); + charsetDecoder.onMalformedInput(CodingErrorAction.REPLACE); + charsetDecoder.onUnmappableCharacter(CodingErrorAction.REPLACE); + return new InputStreamReader(in, charsetDecoder); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/XmlCleaner.java b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XmlCleaner.java similarity index 99% rename from dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/XmlCleaner.java rename to dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XmlCleaner.java index c674031f6..95d1d2402 100644 --- a/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/XmlCleaner.java +++ b/dhp-workflows/dhp-aggregation/src/main/java/eu/dnetlib/dhp/collection/plugin/utils/XmlCleaner.java @@ -1,5 +1,5 @@ -package eu.dnetlib.dhp.collection; +package eu.dnetlib.dhp.collection.plugin.utils; import java.util.HashMap; import java.util.HashSet; diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json new file mode 100644 index 000000000..e9200d3ad --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/input_actionset_parameter.json @@ -0,0 +1,32 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "hmu", + "paramLongName": "hive_metastore_uris", + "paramDescription": "the URI for the hive metastore", + "paramRequired": true + }, + { + "paramName": "o", + "paramLongName": "outputPath", + "paramDescription": "the path of the new ActionSet", + "paramRequired": true + }, + { + "paramName": "sdb", + "paramLongName": "usagestatsdb", + "paramDescription": "the name of the db to be used", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the workingPath where to save the content of the usage_stats table", + "paramRequired": true + } +] \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml new file mode 100644 index 000000000..d262cb6e0 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/config-default.xml @@ -0,0 +1,30 @@ + + + jobTracker + yarnRM + + + nameNode + hdfs://nameservice1 + + + oozie.use.system.libpath + true + + + hiveMetastoreUris + thrift://iis-cdh5-test-m3.ocean.icm.edu.pl:9083 + + + hiveJdbcUrl + jdbc:hive2://iis-cdh5-test-m3.ocean.icm.edu.pl:10000 + + + hiveDbName + openaire + + + oozie.launcher.mapreduce.user.classpath.first + true + + diff --git a/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml new file mode 100644 index 000000000..d94cf7d53 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/main/resources/eu/dnetlib/dhp/actionmanager/usagestats/oozie_app/workflow.xml @@ -0,0 +1,99 @@ + + + + outputPath + the path where to store the actionset + + + usagestatsdb + the name of the db to be used + + + sparkDriverMemory + memory for driver process + + + sparkExecutorMemory + memory for individual executor + + + sparkExecutorCores + number of cores used by single executor + + + oozieActionShareLibForSpark2 + oozie action sharelib for spark 2.* + + + spark2ExtraListeners + com.cloudera.spark.lineage.NavigatorAppListener + spark 2.* extra listeners classname + + + spark2SqlQueryExecutionListeners + com.cloudera.spark.lineage.NavigatorQueryListener + spark 2.* sql query execution listeners classname + + + spark2YarnHistoryServerAddress + spark 2.* yarn history server address + + + spark2EventLogDir + spark 2.* event log dir location + + + + + ${jobTracker} + ${nameNode} + + + mapreduce.job.queuename + ${queueName} + + + oozie.launcher.mapred.job.queue.name + ${oozieLauncherQueueName} + + + oozie.action.sharelib.for.spark + ${oozieActionShareLibForSpark2} + + + + + + + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + + + + yarn + cluster + Produces the atomic action with the usage stats count for results + eu.dnetlib.dhp.actionmanager.usagestats.SparkAtomicActionUsageJob + dhp-aggregation-${projectVersion}.jar + + --executor-memory=${sparkExecutorMemory} + --executor-cores=${sparkExecutorCores} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.warehouse.dir=${sparkSqlWarehouseDir} + + --hive_metastore_uris${hiveMetastoreUris} + --outputPath${outputPath} + --usagestatsdb${usagestatsdb} + --workingPath${workingDir}/usageDb + + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala index 48d0f1497..ff966aaea 100644 --- a/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala +++ b/dhp-workflows/dhp-aggregation/src/main/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTransformation.scala @@ -47,13 +47,18 @@ object DataciteToOAFTransformation { } /** This method should skip record if json contains invalid text - * defined in gile datacite_filter + * defined in file datacite_filter * - * @param json + * @param record : unparsed datacite record + * @param json : parsed record * @return True if the record should be skipped */ - def skip_record(json: String): Boolean = { - datacite_filter.exists(f => json.contains(f)) + def skip_record(record: String, json: org.json4s.JValue): Boolean = { + implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats + datacite_filter.exists(f => record.contains(f)) || (json \\ "publisher") + .extractOrElse[String]("") + .equalsIgnoreCase("FAIRsharing") + } @deprecated("this method will be removed", "dhp") @@ -304,12 +309,13 @@ object DataciteToOAFTransformation { vocabularies: VocabularyGroup, exportLinks: Boolean ): List[Oaf] = { - if (skip_record(input)) - return List() implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats lazy val json = parse(input) + if (skip_record(input, json)) + return List() + val resourceType = (json \ "attributes" \ "types" \ "resourceType").extractOrElse[String](null) val resourceTypeGeneral = (json \ "attributes" \ "types" \ "resourceTypeGeneral").extractOrElse[String](null) diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java new file mode 100644 index 000000000..8aa718bae --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/actionmanager/usagestats/SparkAtomicActionCountJobTest.java @@ -0,0 +1,256 @@ + +package eu.dnetlib.dhp.actionmanager.usagestats; + +import static org.junit.jupiter.api.Assertions.assertEquals; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.stream.Collectors; + +import org.apache.commons.io.FileUtils; +import org.apache.hadoop.io.Text; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.action.AtomicAction; +import eu.dnetlib.dhp.schema.oaf.Result; + +public class SparkAtomicActionCountJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + private static final Logger log = LoggerFactory + .getLogger(SparkAtomicActionCountJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files + .createTempDirectory(SparkAtomicActionCountJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(SparkAtomicActionCountJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(SparkAtomicActionCountJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void testMatch() { + String usageScoresPath = getClass() + .getResource("/eu/dnetlib/dhp/actionmanager/usagestats/usagestatsdb") + .getPath(); + + SparkAtomicActionUsageJob.writeActionSet(spark, usageScoresPath, workingDir.toString() + "/actionSet"); + + final JavaSparkContext sc = new JavaSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .sequenceFile(workingDir.toString() + "/actionSet", Text.class, Text.class) + .map(usm -> OBJECT_MAPPER.readValue(usm._2.getBytes(), AtomicAction.class)) + .map(aa -> (Result) aa.getPayload()); + + Assertions.assertEquals(9, tmp.count()); + + tmp.foreach(r -> Assertions.assertEquals(2, r.getMeasures().size())); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach(u -> Assertions.assertFalse(u.getDataInfo().getDeletedbyinference())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m.getUnit().stream().forEach(u -> Assertions.assertTrue(u.getDataInfo().getInferred())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach(u -> Assertions.assertFalse(u.getDataInfo().getInvisible())))); + + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "measure:usage_counts", + u.getDataInfo().getProvenanceaction().getClassid())))); + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "Inferred by OpenAIRE", + u.getDataInfo().getProvenanceaction().getClassname())))); + + tmp + .foreach( + r -> r + .getMeasures() + .stream() + .forEach( + m -> m + .getUnit() + .stream() + .forEach( + u -> Assertions + .assertEquals( + "count", + u.getKey())))); + + Assertions + .assertEquals( + 1, tmp.filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")).count()); + + Assertions + .assertEquals( + "0", + tmp + .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "5", + tmp + .filter(r -> r.getId().equals("50|dedup_wf_001::53575dc69e9ace947e02d47ecd54a7a6")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + + Assertions + .assertEquals( + "0", + tmp + .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "1", + tmp + .filter(r -> r.getId().equals("50|doi_________::17eda2ff77407538fbe5d3d719b9d1c0")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + + Assertions + .assertEquals( + "2", + tmp + .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("downloads")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + Assertions + .assertEquals( + "6", + tmp + .filter(r -> r.getId().equals("50|doi_________::3085e4c6e051378ca6157fe7f0430c1f")) + .collect() + .get(0) + .getMeasures() + .stream() + .filter(m -> m.getId().equals("views")) + .collect(Collectors.toList()) + .get(0) + .getUnit() + .get(0) + .getValue()); + } + +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java new file mode 100644 index 000000000..6fd101634 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileCollectorPluginTest.java @@ -0,0 +1,61 @@ + +package eu.dnetlib.dhp.collection.plugin.file; + +import java.io.IOException; +import java.util.HashMap; +import java.util.stream.Stream; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeEach; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; +import net.bytebuddy.asm.Advice; + +public class FileCollectorPluginTest { + + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); + + private final ApiDescriptor api = new ApiDescriptor(); + + private FileCollectorPlugin plugin; + + private static final String SPLIT_ON_ELEMENT = "repository"; + + @BeforeEach + public void setUp() throws IOException { + + final String gzipFile = this + .getClass() + .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml") + .getFile(); + + api.setBaseUrl(gzipFile); + + HashMap params = new HashMap<>(); + params.put("splitOnElement", SPLIT_ON_ELEMENT); + + api.setParams(params); + + FileSystem fs = FileSystem.get(new Configuration()); + plugin = new FileCollectorPlugin(fs); + } + + @Test + void test() throws CollectorException { + + final Stream stream = plugin.collect(api, new AggregatorReport()); + + stream.limit(10).forEach(s -> { + Assertions.assertTrue(s.length() > 0); + log.info(s); + }); + } +} diff --git a/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java new file mode 100644 index 000000000..dc24d6f13 --- /dev/null +++ b/dhp-workflows/dhp-aggregation/src/test/java/eu/dnetlib/dhp/collection/plugin/file/FileGZipCollectorPluginTest.java @@ -0,0 +1,68 @@ + +package eu.dnetlib.dhp.collection.plugin.file; + +import java.io.File; +import java.io.IOException; +import java.nio.file.Files; +import java.util.HashMap; +import java.util.Objects; +import java.util.stream.Stream; + +import org.apache.hadoop.conf.Configuration; +import org.apache.hadoop.fs.FileSystem; +import org.apache.hadoop.fs.LocalFileSystem; +import org.junit.jupiter.api.*; +import org.junit.jupiter.api.extension.ExtendWith; +import org.mockito.Mockito; +import org.mockito.junit.jupiter.MockitoExtension; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import eu.dnetlib.dhp.collection.ApiDescriptor; +import eu.dnetlib.dhp.common.aggregation.AggregatorReport; +import eu.dnetlib.dhp.common.collection.CollectorException; + +@TestMethodOrder(MethodOrderer.OrderAnnotation.class) +@ExtendWith(MockitoExtension.class) +public class FileGZipCollectorPluginTest { + + private static final Logger log = LoggerFactory.getLogger(FileGZipCollectorPluginTest.class); + + private final ApiDescriptor api = new ApiDescriptor(); + + private FileGZipCollectorPlugin plugin; + + private static final String SPLIT_ON_ELEMENT = "repository"; + + @BeforeEach + public void setUp() throws IOException { + + final String gzipFile = Objects + .requireNonNull( + this + .getClass() + .getResource("/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz")) + .getFile(); + + api.setBaseUrl(gzipFile); + + HashMap params = new HashMap<>(); + params.put("splitOnElement", SPLIT_ON_ELEMENT); + + api.setParams(params); + + FileSystem fs = FileSystem.get(new Configuration()); + plugin = new FileGZipCollectorPlugin(fs); + } + + @Test + void test() throws CollectorException { + + final Stream stream = plugin.collect(api, new AggregatorReport()); + + stream.limit(10).forEach(s -> { + Assertions.assertTrue(s.length() > 0); + log.info(s); + }); + } +} 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Nottingham + OpenDOAR data is available for re-use under a Creative Commons Attribution-Non-Commercial-Share Alike licence + + + Architektur-Informatik + + Y + http://architektur-informatik.scix.net/ + http://architektur-informatik.scix.net/cgi-bin/works/OAI + + + + + Arbeitskreis Architekturinformatik + AK AI + Y + http://www.architektur-informatik.org/ + + + AT + Austria + + 46.783300 + 12.950000 + + + This is a German language repository on Computer Science. 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Assume no rights at all have been granted. + + + + Submission + Submission policies defined + + Items may only be deposited by accredited members of the institution + Authors may only submit their own work for archiving. + The administrator only vets items for relevance to the scope of the repository + The validity and authenticity of the content of submissions is not checked. + No embargo policy defined. + Any copyright violations are entirely the responsibility of the authors/depositors. + If the repository receives proof of copyright violation, the relevant item will be removed immediately. + + + + Preserve + Preservation policies not stated + + No preservation policy defined. + + + + + + H Hracovec + Site Administrator + hrachov@philo.at + + + + + + Elektronische Publikationen der Wirtschaftsuniversität Wien + Epub WU + Y + http://epub.wu.ac.at/ + http://epub.wu.ac.at/cgi/oai2 + Universtätsbibliothek (University Library) + + Y + http://www.wu.ac.at/library + Wirtschaftsuniversität Wien (Vienna University of Economics) + WU + Y + http://www.wu.ac.at/ + Augasse 2-6, A-Wien + + AT + Austria + + 48.230000 + 16.357000 + 0131-3364990 + + This is the institutional repository of the WU Vienna University of Economics and Business. It provides access to the research output of the institution. Documents are available in full text. 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However only a very small proportion of material is available via Open Access as this site is mainly concerned with subscription-only access to its eBook and printed publications. As such that material which is offered freely is intended to induce a purchasing activity from the reader. The main site interface is available in English or German, however the supporting information and help is in the latter only. Users may set up RSS feeds to be alerted to new content. + Partners: Verlag der Österreichischen Akademie der Wissenschaften + + 2012-02-27 + 2006 + Institutional + Operational + Hyperwave + + + + C + Multidisciplinary + + + + + de + German + + + en + English + + + + Books, chapters and sections + + + + Content + Content policies explicitly undefined + + This is an institutional or departmental repository. + No content policy defined. + + + + Metadata + Metadata re-use policy explicitly undefined + + Anyone may access the metadata free of charge. + No metadata re-use policy defined. Assume no rights at all have been granted. + + + + Data + Full data item policies explicitly undefined + + Anyone may access full items free of charge. + No full-item re-use policy defined. Assume no rights at all have been granted. + + + + Submission + Submission policies explicitly undefined + + No submission policy defined. + + + + Preserve + Preservation policies not stated + + No preservation policy defined. + + + + + + Herwig Stöger + Administrator + herwig.stoeger@oeaw.ac.at + + + + + + European Research Papers Archive + ERPA + Y + http://eiop.or.at/erpa/ + http://eiop.or.at/cgi-bin/oaiserv.pl + + + + + European Communities Studies Association Austria + ECSA Austria + Y + http://www2.wu-wien.ac.at/ecsa/ + Institut für Technikfolgen-Abschätzung, Österreichische Akademie der Wissenschaften, Strohgasse 45/5, A-1030 Wien + + AT + Austria + + 48.230100 + 16.359200 + +43 1 51581 6583 + +43 1 710 98 83 + This site is an aggregating repository that contains a collection of research papers from ten European institutions. The site contains working papers on European Integration. The site interface is in English but several papers are written in French and German. + + 1098 + 2007-07-17 + + Aggregating + Operational + + + + + Cog + Geography and Regional Studies + + + Cub + Business and Economics + + + Cup + Law and Politics + + + + + en + English + + + fr + French + + + de + German + + + + Journal articles + Unpublished reports and working papers + + + + Content + Content policies defined + + This is a multi-institution subject-based repository. + Subject Specialities: + + Multidisciplinary + History and Archaeology + Social Sciences General + Business and Economics + Law and Politics + + + The repository is restricted to: + + Journal articles + Conference and workshop papers + Unpublished reports and working papers + + + Deposited items may include: + + submitted versions (as sent to journals for peer-review) + accepted versions (author's final peer-reviewed drafts) + published versions (publisher-created files) + + + Principal Languages: English; German + For more information, please see webpage: http://eiop.or.at/erpa/erpainfo.htm + + + + Metadata + Metadata re-use permitted for not-for-profit purposes + + Anyone may access the metadata free of charge. + The metadata may be re-used in any medium without prior permission for not-for-profit purposes provided: + + the OAI Identifier or a link to the original metadata record are given + the repository is mentioned + + + + + + Data + Re-use of full data items permitted for not-for-profit purposes + + Anyone may access full items free of charge. + Copies of full items generally can be: + + displayed or performed + for personal research or study purposes without prior permission or charge. + + + This repository is not the publisher; it is merely the online archive. + + + + Submission + Submission policies defined + + Items may only be deposited by accredited members of the institution, or their delegated agents. + Eligible depositors must deposit bibliographic metadata for all their publications. + Eligible depositors must deposit full texts of all their publications. + No moderation policy defined. Assume nothing has been vetted. + The validity and authenticity of the content of submissions is the sole responsibility of the depositor. + No embargo policy defined. + Any copyright violations are entirely the responsibility of the authors/depositors. + For more information see webpage: http://eiop.or.at/erpa/policy.htm + + + + Preserve + Preservation policies unclearly stated + + No retention period defined. + The repository will try to ensure continued readability and accessibility. + No file preservation policy defined. + No withdrawal policy defined. + Withdrawn items are deleted entirely from the database. + Withdrawn items' identifiers/URLs are not retained. + In the event of the repository being closed down, the database will be transferred to another appropriate archive. + + + + + + Michael Nentwich + Site Administrator + mnent@oeaw.ac.at + + + + + + OTHES + + Y + http://othes.univie.ac.at/ + https://othes.univie.ac.at/secure/cgi/oai2 + + + + + Universität Wien + + Y + http://www.univie.ac.at/ + Fakultät für Philosopohie und Bildungswissenschaft, Universitätsstraße 7, A-1010 Wien + + AT + Austria + + 48.209190 + 16.372740 + + + This is an institutional repository for the University of Vienna providing access to the thesis and dissertation output of the university. Users may set up Atom and RSS feeds to be alerted to new content. + + 8066 + 2010-04-16 + + Institutional + Operational + EPrints + 3.0.1-beta-2 + + + C + Multidisciplinary + + + + + de + German + + + + Theses and dissertations + + + + Content + Content policies explicitly undefined + + This is an institutional or departmental repository. + No content policy defined. + + + + Metadata + Metadata re-use policy explicitly undefined + + Anyone may access the metadata free of charge. + No metadata re-use policy defined. Assume no rights at all have been granted. + + + + Data + Full data item policies explicitly undefined + + Anyone may access full items free of charge. + No full-item re-use policy defined. Assume no rights at all have been granted. + + + + Submission + Submission policies explicitly undefined + + No submission policy defined. + + + + Preserve + Preservation policies explicitly undefined + + No preservation policy defined. + + + + + + Adelheid Mayer + Administrator + adelheid.mayer@univie.ac.at + + + + + + thesis-help.ub@univie.ac.at + + + + + + Permanent Hosting, Archiving and Indexing of Digital Resources and Assets + Phaidra + N + https://phaidra.univie.ac.at/ + + + + + + Universität Wien + + Y + http://www.univie.ac.at/ + Fakultät für Philosopohie und Bildungswissenschaft, Universitätsstraße 7, A-1010 Wien + + AT + Austria + + 48.209190 + 16.372740 + + + This site provides access to the digitised copies of the institutions collection as well as teaching material. The interface is in German. + + + 2010-02-17 + + Institutional + Operational + Fedora + + + + C + Multidisciplinary + + + + + de + German + + + + Books, chapters and sections + Learning Objects + Multimedia and audio-visual materials + + + + Content + Content policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Metadata + Metadata re-use policy explicitly undefined + + No policy registered in OpenDOAR. + + + + Data + Full data item policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Submission + Submission policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Preserve + Preservation policies explicitly undefined + + No policy registered in OpenDOAR. + + + + + + Paolo Budroni + Administrator + paolo.budroni@univie.ac.at + + + + + + textfeld + + Y + http://www.textfeld.ac.at/ + + + + + + textfeld society for advancement of academic potential + + Y + http://textfeld.ac.at/ + Wien + + AT + Austria + + 48.239300 + 16.369600 + + + This site provides access to publications by students and young scholars of all fields. Interface is in German. + + 514 + 2012-02-13 + + Aggregating + Operational + + + + + C + Multidisciplinary + + + + + de + German + + + + Journal articles + Theses and dissertations + + + + Content + Content policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Metadata + Metadata re-use policy explicitly undefined + + No policy registered in OpenDOAR. + + + + Data + Full data item policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Submission + Submission policies explicitly undefined + + No policy registered in OpenDOAR. + + + + Preserve + Preservation policies explicitly undefined + + No policy registered in OpenDOAR. + + + + + + + Repository of Belarusian National Technical University (BNTU) + + Y + http://rep.bntu.by/ + + + + + + Belarusian National Technical University + + Y + http://www.bntu.by/ + + + BY + Belarus + + 53.922100 + 27.590700 + + + This site provides access to the research output of the institution. The interface is available in Russian and English. Users may set up RSS feeds to be alerted to new content. + + 286 + 2012-01-26 + + Institutional + Operational + DSpace + + + + C + Multidisciplinary + + + + + en + English + + + ru + Russian + + + + Journal articles + Books, chapters and sections + Learning Objects + + + + + Alexey Skalaban + Administrator + skalaban@gmail.com + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz new file mode 100644 index 000000000..f783b69e7 Binary files /dev/null and b/dhp-workflows/dhp-aggregation/src/test/resources/eu/dnetlib/dhp/collection/plugin/file/opendoar.xml.gz differ diff --git a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala index 8e41de83c..31784c7e9 100644 --- a/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala +++ b/dhp-workflows/dhp-aggregation/src/test/scala/eu/dnetlib/dhp/datacite/DataciteToOAFTest.scala @@ -107,4 +107,19 @@ class DataciteToOAFTest extends AbstractVocabularyTest { } + @Test + def testFilter(): Unit = { + val record = Source + .fromInputStream( + getClass.getResourceAsStream("/eu/dnetlib/dhp/actionmanager/datacite/record_fairsharing.json") + ) + .mkString + + val mapper = new ObjectMapper().enable(SerializationFeature.INDENT_OUTPUT) + val res: List[Oaf] = DataciteToOAFTransformation.generateOAF(record, 0L, 0L, vocabularies, true) + + assertTrue(res.isEmpty) + + } + } diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala index 72b93749b..3315fc41d 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/SparkGenerateDoiBoost.scala @@ -59,54 +59,6 @@ object SparkGenerateDoiBoost { val workingDirPath = parser.get("workingPath") val openaireOrganizationPath = parser.get("openaireOrganizationPath") - val crossrefAggregator = new Aggregator[(String, Publication), Publication, Publication] with Serializable { - override def zero: Publication = null - - override def reduce(b: Publication, a: (String, Publication)): Publication = { - - if (b == null) { - if (a != null && a._2 != null) { - a._2.setId(a._1) - return a._2 - } - } else { - if (a != null && a._2 != null) { - b.mergeOAFDataInfo(a._2) - b.mergeFrom(a._2) - b.setId(a._1) - val authors = AuthorMerger.mergeAuthor(b.getAuthor, a._2.getAuthor) - b.setAuthor(authors) - return b - } - } - new Publication - } - - override def merge(b1: Publication, b2: Publication): Publication = { - if (b1 == null) { - if (b2 != null) - return b2 - } else { - if (b2 != null) { - b1.mergeOAFDataInfo(b2) - b1.mergeFrom(b2) - val authors = AuthorMerger.mergeAuthor(b1.getAuthor, b2.getAuthor) - b1.setAuthor(authors) - if (b2.getId != null && b2.getId.nonEmpty) - b1.setId(b2.getId) - return b1 - } - } - new Publication - } - - override def finish(reduction: Publication): Publication = reduction - - override def bufferEncoder: Encoder[Publication] = Encoders.kryo[Publication] - - override def outputEncoder: Encoder[Publication] = Encoders.kryo[Publication] - } - implicit val mapEncoderPub: Encoder[Publication] = Encoders.kryo[Publication] implicit val mapEncoderOrg: Encoder[Organization] = Encoders.kryo[Organization] implicit val mapEncoderDataset: Encoder[OafDataset] = Encoders.kryo[OafDataset] @@ -332,4 +284,4 @@ object SparkGenerateDoiBoost { .save(s"$workingDirPath/doiBoostOrganization") } -} +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala index b4d6d67e2..9eec9e759 100644 --- a/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala +++ b/dhp-workflows/dhp-doiboost/src/main/scala/eu/dnetlib/doiboost/crossref/Crossref2Oaf.scala @@ -2,7 +2,7 @@ package eu.dnetlib.doiboost.crossref import eu.dnetlib.dhp.schema.common.ModelConstants import eu.dnetlib.dhp.schema.oaf._ -import eu.dnetlib.dhp.schema.oaf.utils.{IdentifierFactory, OafMapperUtils} +import eu.dnetlib.dhp.schema.oaf.utils.{GraphCleaningFunctions, IdentifierFactory, OafMapperUtils} import eu.dnetlib.dhp.utils.DHPUtils import eu.dnetlib.doiboost.DoiBoostMappingUtil import eu.dnetlib.doiboost.DoiBoostMappingUtil._ @@ -280,10 +280,10 @@ case object Crossref2Oaf { instance.setDateofacceptance(asField(createdDate.getValue)) } val s: List[String] = List("https://doi.org/" + doi) -// val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct -// if (links.nonEmpty) { -// instance.setUrl(links.asJava) -// } + // val links: List[String] = ((for {JString(url) <- json \ "link" \ "URL"} yield url) ::: List(s)).filter(p => p != null && p.toLowerCase().contains(doi.toLowerCase())).distinct + // if (links.nonEmpty) { + // instance.setUrl(links.asJava) + // } if (s.nonEmpty) { instance.setUrl(s.asJava) } @@ -576,14 +576,19 @@ case object Crossref2Oaf { def extractDate(dt: String, datePart: List[List[Int]]): String = { if (StringUtils.isNotBlank(dt)) - return dt + return GraphCleaningFunctions.cleanDate(dt) if (datePart != null && datePart.size == 1) { val res = datePart.head if (res.size == 3) { val dp = f"${res.head}-${res(1)}%02d-${res(2)}%02d" if (dp.length == 10) { - return dp + return GraphCleaningFunctions.cleanDate(dp) } + } else if (res.size == 2) { + val dp = f"${res.head}-${res(1)}%02d-01" + return GraphCleaningFunctions.cleanDate(dp) + } else if (res.size == 1) { + return GraphCleaningFunctions.cleanDate(s"${res.head}-01-01") } } null diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json new file mode 100644 index 000000000..48a3777b7 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/article_nojournal.json @@ -0,0 +1,368 @@ + +{ + + "indexed": { + "date-parts": [ + [ + 2022, + 4, + 22 + ] + ], + "date-time": "2022-04-22T15:30:54Z", + "timestamp": 1650641454218 + }, + "reference-count": 31, + "publisher": "Cambridge University Press (CUP)", + "issue": "2", + "license": [ + { + "start": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ], + "date-time": "2017-08-22T00:00:00Z", + "timestamp": 1503360000000 + }, + "content-version": "unspecified", + "delay-in-days": 21, + "URL": "https://www.cambridge.org/core/terms" + } + ], + "content-domain": { + "domain": [ + + ], + "crossmark-restriction": false + }, + "short-container-title": [ + "Dance Res. J." + ], + "published-print": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + }, + "abstract": "Gaga, a practice developed by Israeli choreographer Ohad Naharin, is one of the most popular training methods on the global dance market. Structured as a metatechnique, or a system for negotiating techniques within one's body, Gaga teaches students to both draw on and reject multiple movement techniques to create their own movement. I consider how the paradigms of choreography, technique, and improvisation are blurred together in the pedagogical model of a metatechnique and how training dancers to shift between choreographer, dancer, and improviser has significant ramifications for understanding their agency. The metatechnique model of Gaga falls in line with neoliberal values of efficiency and a wide range of skills and knowledge; this analysis provides an understanding of recent trends in dance training in relation to contemporary political and socioeconomic structures.", + "DOI": "10.1017/s0149767717000183", + "type": "journal-article", + "created": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ], + "date-time": "2017-08-22T13:32:38Z", + "timestamp": 1503408758000 + }, + "page": "26-43", + "source": "Crossref", + "is-referenced-by-count": 10, + "title": [ + "Gaga as Metatechnique: Negotiating Choreography, Improvisation, and Technique in a Neoliberal Dance Market" + ], + "prefix": "10.1017", + "volume": "49", + "author": [ + { + "given": "Meghan", + "family": "Quinlan", + "sequence": "first", + "affiliation": [ + + ] + } + ], + "member": "56", + "published-online": { + "date-parts": [ + [ + 2017, + 8, + 22 + ] + ] + }, + "reference": [ + { + "key": "S0149767717000183_ref22", + "first-page": "38", + "article-title": "‘I Don't Want to do African … What About My Technique?’: Transforming Dancing Places into Spaces in the Academy", + "volume": "4", + "author": "Monroe", + "year": "2011", + "journal-title": "The Journal of Pan African Studies" + }, + { + "key": "S0149767717000183_ref8", + "volume-title": "Discipline and Punish: The Birth of the Prison", + "author": "Foucault", + "year": "1995" + }, + { + "key": "S0149767717000183_ref24", + "volume-title": "Sharing the Dance: Contact Improvisation and American Culture", + "author": "Novack", + "year": "1990" + }, + { + "key": "S0149767717000183_ref26", + "doi-asserted-by": "publisher", + "DOI": "10.1215/9780822387879" + }, + { + "key": "S0149767717000183_ref10", + "doi-asserted-by": "publisher", + "DOI": "10.1080/01472526.2015.1085759" + }, + { + "key": "S0149767717000183_ref4", + "doi-asserted-by": "crossref", + "first-page": "235", + "volume-title": "Meaning in Motion", + "author": "Foster", + "year": "1997", + "DOI": "10.1215/9780822397281-013" + }, + { + "key": "S0149767717000183_ref17", + "doi-asserted-by": "publisher", + "DOI": "10.1093/acprof:oso/9780199360369.001.0001" + }, + { + "key": "S0149767717000183_ref30", + "volume-title": "The Precariat: The New Dangerous Class", + "author": "Standing", + "year": "2011" + }, + { + "key": "S0149767717000183_ref7", + "volume-title": "Choreographing Empathy: Kinesthesia in Performance", + "author": "Foster", + "year": "2011" + }, + { + "key": "S0149767717000183_ref14", + "volume-title": "A Brief History of Neoliberalism", + "author": "Harvey", + "year": "2007" + }, + { + "key": "S0149767717000183_ref27", + "unstructured": "Quinlan Meghan . 2016. “Gaga as Politics: A Case Study of Contemporary Dance Training.” PhD diss., University of California, Riverside." + }, + { + "key": "S0149767717000183_ref11", + "first-page": "xiii", + "volume-title": "Taken by Surprise: A Dance Improvisation Reader", + "author": "Gere", + "year": "2003" + }, + { + "key": "S0149767717000183_ref13", + "volume-title": "Declaration", + "author": "Hardt", + "year": "2012" + }, + { + "key": "S0149767717000183_ref29", + "doi-asserted-by": "publisher", + "DOI": "10.1057/9780230236844_9" + }, + { + "key": "S0149767717000183_ref5", + "doi-asserted-by": "publisher", + "DOI": "10.1057/9780230236844_6" + }, + { + "key": "S0149767717000183_ref28", + "doi-asserted-by": "publisher", + "DOI": "10.1017/S0149767700000528" + }, + { + "key": "S0149767717000183_ref12", + "doi-asserted-by": "publisher", + "DOI": "10.3998/mpub.287881" + }, + { + "key": "S0149767717000183_ref18", + "first-page": "135", + "volume-title": "Taken by Surprise: A Dance Improvisation Reader", + "author": "Marks", + "year": "2003" + }, + { + "key": "S0149767717000183_ref3", + "doi-asserted-by": "crossref", + "volume-title": "Bodies That Matter: On the Discursive Limits of Sex", + "author": "Butler", + "year": "2011", + "DOI": "10.4324/9780203828274" + }, + { + "key": "S0149767717000183_ref32", + "volume-title": "Choreographing Difference: The Body and Identity in Contemporary Dance", + "author": "Albright", + "year": "1997" + }, + { + "key": "S0149767717000183_ref16", + "doi-asserted-by": "publisher", + "DOI": "10.1017/S0149767714000163" + }, + { + "key": "S0149767717000183_ref15", + "doi-asserted-by": "publisher", + "DOI": "10.2307/1477803" + }, + { + "key": "S0149767717000183_ref21", + "first-page": "455", + "volume-title": "Incorporations", + "author": "Mauss", + "year": "1992" + }, + { + "key": "S0149767717000183_ref1", + "volume-title": "The Body Eclectic: Evolving Practices in Dance Training", + "author": "Bales", + "year": "2008" + }, + { + "key": "S0149767717000183_ref9", + "unstructured": "Gaga Movement Ltd. 2016. Gaga People. Dancers. Accessed June 28, 2016. http://gagapeople.com/english/." + }, + { + "key": "S0149767717000183_ref19", + "volume-title": "Critical Moves: Dance Studies in Theory and Politics", + "author": "Martin", + "year": "1998" + }, + { + "key": "S0149767717000183_ref2", + "volume-title": "Undoing the Demos: Neoliberalism's Stealth Revolution", + "author": "Brown", + "year": "2015" + }, + { + "key": "S0149767717000183_ref20", + "doi-asserted-by": "publisher", + "DOI": "10.1162/DRAM_a_00214" + }, + { + "key": "S0149767717000183_ref6", + "doi-asserted-by": "publisher", + "DOI": "10.1215/01610775-2009-016" + }, + { + "key": "S0149767717000183_ref23", + "doi-asserted-by": "publisher", + "DOI": "10.1093/acprof:oso/9780190201661.001.0001" + }, + { + "key": "S0149767717000183_ref25", + "volume-title": "Flexible Citizenship: The Cultural Logics of Transnationality", + "author": "Ong", + "year": "1999" + } + ], + "container-title": [ + "Dance Research Journal" + ], + "original-title": [ + + ], + "language": "en", + "link": [ + { + "URL": "https://www.cambridge.org/core/services/aop-cambridge-core/content/view/S0149767717000183", + "content-type": "unspecified", + "content-version": "vor", + "intended-application": "similarity-checking" + } + ], + "deposited": { + "date-parts": [ + [ + 2020, + 10, + 16 + ] + ], + "date-time": "2020-10-16T01:00:32Z", + "timestamp": 1602810032000 + }, + "score": 1, + "resource": { + "primary": { + "URL": "https://www.cambridge.org/core/product/identifier/S0149767717000183/type/journal_article" + } + }, + "subtitle": [ + + ], + "short-title": [ + + ], + "issued": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + }, + "references-count": 31, + "journal-issue": { + "issue": "2", + "published-print": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + } + }, + "alternative-id": [ + "S0149767717000183" + ], + "URL": "http://dx.doi.org/10.1017/s0149767717000183", + "relation": { + + }, + "ISSN": [ + "0149-7677", + "1940-509X" + ], + "issn-type": [ + { + "value": "0149-7677", + "type": "print" + }, + { + "value": "1940-509X", + "type": "electronic" + } + ], + "subject": [ + "Visual Arts and Performing Arts" + ], + "published": { + "date-parts": [ + [ + 2017, + 8 + ] + ] + } + } diff --git a/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json new file mode 100644 index 000000000..d74b2c167 --- /dev/null +++ b/dhp-workflows/dhp-doiboost/src/test/resources/eu/dnetlib/doiboost/crossref/issue_date.json @@ -0,0 +1,330 @@ +{ + "indexed":{ + "date-parts":[ + [ + 2022, + 4, + 14 + ] + ], + "date-time":"2022-04-14T11:27:30Z", + "timestamp":1649935650109 + }, + "reference-count":22, + "publisher":"SAGE Publications", + "issue":"2", + "license":[ + { + "start":{ + "date-parts":[ + [ + 1980, + 4, + 1 + ] + ], + "date-time":"1980-04-01T00:00:00Z", + "timestamp":323395200000 + }, + "content-version":"tdm", + "delay-in-days":0, + "URL":"http:\/\/journals.sagepub.com\/page\/policies\/text-and-data-mining-license" + } + ], + "content-domain":{ + "domain":[ + + ], + "crossmark-restriction":false + }, + "short-container-title":[ + "Perception" + ], + "published-print":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + }, + "abstract":" To answer the question \u2018What is suppressed during binocular rivalry?\u2019 a series of three experiments was performed. In the first experiment observers viewed binocular rivalry between orthogonally oriented patterns. When the dominant and suppressed patterns were interchanged between the eyes observers continued seeing with the dominant eye, indicating that an eye, not a pattern, is suppressed during rivalry. In a second experiment it was found that a suppressed eye was able to contribute to stereopsis. A third experiment demonstrated that the predominance of an eye could be influenced by prior adaptation of the other eye, indicating that binocular mechanisms participate in the rivalry process. <\/jats:p>", + "DOI":"10.1068\/p090223", + "type":"journal-article", + "created":{ + "date-parts":[ + [ + 2007, + 1, + 23 + ] + ], + "date-time":"2007-01-23T15:21:36Z", + "timestamp":1169565696000 + }, + "page":"223-231", + "source":"Crossref", + "is-referenced-by-count":123, + "title":[ + "What is Suppressed during Binocular Rivalry?" + ], + "prefix":"10.1177", + "volume":"9", + "author":[ + { + "given":"Randolph", + "family":"Blake", + "sequence":"first", + "affiliation":[ + { + "name":"Cresap Neuroscience Laboratory, Northwestern University, Evanston, Illinois 60201, USA" + } + ] + }, + { + "given":"David H", + "family":"Westendorf", + "sequence":"additional", + "affiliation":[ + { + "name":"Department of Psychology, University of Arkansas, Fayetteville, Arkansas 72701, USA" + } + ] + }, + { + "given":"Randall", + "family":"Overton", + "sequence":"additional", + "affiliation":[ + { + "name":"Department of Psychology, Illinois State University, Normal, Illinois 61761, USA" + } + ] + } + ], + "member":"179", + "published-online":{ + "date-parts":[ + [ + 2016, + 6, + 25 + ] + ] + }, + "reference":[ + { + "key":"bibr1-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1136\/bjo.37.1.37" + }, + { + "key":"bibr2-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/0096-1523.5.2.315" + }, + { + "key":"bibr3-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(74)90065-0" + }, + { + "key":"bibr4-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1068\/p080143" + }, + { + "key":"bibr5-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(70)90036-2" + }, + { + "key":"bibr6-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1969.sp008862" + }, + { + "key":"bibr7-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1972.sp010006" + }, + { + "key":"bibr8-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1146\/annurev.ps.23.020172.002213" + }, + { + "key":"bibr9-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1126\/science.166.3902.245" + }, + { + "key":"bibr10-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/h0075805" + }, + { + "key":"bibr11-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1968.sp008552" + }, + { + "key":"bibr12-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1113\/jphysiol.1965.sp007784" + }, + { + "key":"bibr13-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/h0032455" + }, + { + "key":"bibr14-p090223", + "volume-title":"Treatise on Physiological Optics", + "volume":"3", + "author":"von Helmholtz H", + "year":"1866", + "edition":"3" + }, + { + "key":"bibr15-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1068\/p040125" + }, + { + "key":"bibr16-p090223", + "volume-title":"On Binocular Rivalry", + "author":"Levelt W J M", + "year":"1965" + }, + { + "key":"bibr17-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1001\/archopht.1935.00840020011001" + }, + { + "key":"bibr18-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03205796" + }, + { + "key":"bibr19-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03210180" + }, + { + "key":"bibr20-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1037\/0033-2909.85.2.376" + }, + { + "key":"bibr21-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.1016\/0042-6989(79)90169-X" + }, + { + "key":"bibr22-p090223", + "doi-asserted-by":"publisher", + "DOI":"10.3758\/BF03210465" + } + ], + "container-title":[ + "Perception" + ], + "original-title":[ + + ], + "language":"en", + "link":[ + { + "URL":"http:\/\/journals.sagepub.com\/doi\/pdf\/10.1068\/p090223", + "content-type":"application\/pdf", + "content-version":"vor", + "intended-application":"text-mining" + }, + { + "URL":"http:\/\/journals.sagepub.com\/doi\/pdf\/10.1068\/p090223", + "content-type":"unspecified", + "content-version":"vor", + "intended-application":"similarity-checking" + } + ], + "deposited":{ + "date-parts":[ + [ + 2021, + 12, + 3 + ] + ], + "date-time":"2021-12-03T11:49:48Z", + "timestamp":1638532188000 + }, + "score":1, + "resource":{ + "primary":{ + "URL":"http:\/\/journals.sagepub.com\/doi\/10.1068\/p090223" + } + }, + "subtitle":[ + + ], + "short-title":[ + + ], + "issued":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + }, + "references-count":22, + "journal-issue":{ + "issue":"2", + "published-print":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + } + }, + "alternative-id":[ + "10.1068\/p090223" + ], + "URL":"http:\/\/dx.doi.org\/10.1068\/p090223", + "relation":{ + + }, + "ISSN":[ + "0301-0066", + "1468-4233" + ], + "issn-type":[ + { + "value":"0301-0066", + "type":"print" + }, + { + "value":"1468-4233", + "type":"electronic" + } + ], + "subject":[ + "Artificial Intelligence", + "Sensory Systems", + "Experimental and Cognitive Psychology", + "Ophthalmology" + ], + "published":{ + "date-parts":[ + [ + 1980, + 4 + ] + ] + } +} \ No newline at end of file diff --git a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala index 8124a5aae..98b5b708e 100644 --- a/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala +++ b/dhp-workflows/dhp-doiboost/src/test/scala/eu/dnetlib/dhp/doiboost/crossref/CrossrefMappingTest.scala @@ -73,6 +73,20 @@ class CrossrefMappingTest { } + @Test + def crossrefIssueDateTest(): Unit = { + val json = + Source.fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/issue_date.json")).mkString + assertNotNull(json) + assertFalse(json.isEmpty) + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Result]) + + println(mapper.writeValueAsString(items.head)) + } + @Test def testOrcidID(): Unit = { val json = Source @@ -82,7 +96,7 @@ class CrossrefMappingTest { .mkString assertNotNull(json) - assertFalse(json.isEmpty); + assertFalse(json.isEmpty) val resultList: List[Oaf] = Crossref2Oaf.convert(json) @@ -461,6 +475,31 @@ class CrossrefMappingTest { } + @Test + def testConvertFromCrossRef2OafIssue(): Unit = { + val json = Source + .fromInputStream(getClass.getResourceAsStream("/eu/dnetlib/doiboost/crossref/article_nojournal.json")) + .mkString + assertNotNull(json) + + assertFalse(json.isEmpty); + + val resultList: List[Oaf] = Crossref2Oaf.convert(json) + + assertTrue(resultList.nonEmpty) + + val items = resultList.filter(p => p.isInstanceOf[Publication]) + + assert(items.nonEmpty) + assert(items.size == 1) + val pub: Publication = items.head.asInstanceOf[Publication] + + assertNotNull(pub.getJournal.getIssnPrinted) + assertNotNull(pub.getJournal.getIssnOnline) + assertNotNull(pub.getJournal.getName) + + } + @Test def testSetDateOfAcceptanceCrossRef2Oaf(): Unit = { diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java new file mode 100644 index 000000000..b9de5dd11 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/bulktag/SparkEoscTag.java @@ -0,0 +1,251 @@ + +package eu.dnetlib.dhp.bulktag; + +import static eu.dnetlib.dhp.PropagationConstant.readPath; +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.util.*; +import java.util.function.Function; +import java.util.stream.Collectors; +import java.util.stream.Stream; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.*; +import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; + +public class SparkEoscTag { + private static final Logger log = LoggerFactory.getLogger(SparkEoscTag.class); + public static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + public static final Qualifier EOSC_QUALIFIER = OafMapperUtils + .qualifier( + "EOSC", + "European Open Science Cloud", + ModelConstants.DNET_SUBJECT_TYPOLOGIES, ModelConstants.DNET_SUBJECT_TYPOLOGIES); + public static final DataInfo EOSC_DATAINFO = OafMapperUtils + .dataInfo( + false, "propagation", true, false, + OafMapperUtils + .qualifier( + "propagation:subject", "Inferred by OpenAIRE", + ModelConstants.DNET_PROVENANCE_ACTIONS, ModelConstants.DNET_PROVENANCE_ACTIONS), + "0.9"); + public final static StructuredProperty EOSC_NOTEBOOK = OafMapperUtils + .structuredProperty( + "EOSC::Jupyter Notebook", EOSC_QUALIFIER, EOSC_DATAINFO); + public final static StructuredProperty EOSC_GALAXY = OafMapperUtils + .structuredProperty( + "EOSC::Galaxy Workflow", EOSC_QUALIFIER, EOSC_DATAINFO); + public final static StructuredProperty EOSC_TWITTER = OafMapperUtils + .structuredProperty( + "EOSC::Twitter Data", EOSC_QUALIFIER, EOSC_DATAINFO); + + public static void main(String[] args) throws Exception { + String jsonConfiguration = IOUtils + .toString( + SparkEoscTag.class + .getResourceAsStream( + "/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json")); + + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + final String inputPath = parser.get("sourcePath"); + log.info("inputPath: {}", inputPath); + + final String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + SparkConf conf = new SparkConf(); + + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + execEoscTag(spark, inputPath, workingPath); + + }); + } + + private static void execEoscTag(SparkSession spark, String inputPath, String workingPath) { + + readPath(spark, inputPath + "/software", Software.class) + .map((MapFunction) s -> { + List sbject; + if (!Optional.ofNullable(s.getSubject()).isPresent()) + s.setSubject(new ArrayList<>()); + sbject = s.getSubject(); + + if (containsCriteriaNotebook(s)) { + sbject.add(EOSC_NOTEBOOK); + if (sbject.stream().anyMatch(sb -> sb.getValue().equals("EOSC Jupyter Notebook"))) { + sbject = sbject.stream().map(sb -> { + if (sb.getValue().equals("EOSC Jupyter Notebook")) { + return null; + } + return sb; + }).filter(Objects::nonNull).collect(Collectors.toList()); + s.setSubject(sbject); + } + } + if (containsCriteriaGalaxy(s)) { + sbject.add(EOSC_GALAXY); + } + return s; + }, Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/software"); + + readPath(spark, workingPath + "/software", Software.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/software"); + + readPath(spark, inputPath + "/otherresearchproduct", OtherResearchProduct.class) + .map((MapFunction) orp -> { + List sbject; + if (!Optional.ofNullable(orp.getSubject()).isPresent()) + orp.setSubject(new ArrayList<>()); + sbject = orp.getSubject(); + if (containsCriteriaGalaxy(orp)) { + sbject.add(EOSC_GALAXY); + } + if (containscriteriaTwitter(orp)) { + sbject.add(EOSC_TWITTER); + } + return orp; + }, Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/otherresearchproduct"); + + readPath(spark, workingPath + "/otherresearchproduct", OtherResearchProduct.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/otherresearchproduct"); + + readPath(spark, inputPath + "/dataset", Dataset.class) + .map((MapFunction) d -> { + List sbject; + if (!Optional.ofNullable(d.getSubject()).isPresent()) + d.setSubject(new ArrayList<>()); + sbject = d.getSubject(); + if (containscriteriaTwitter(d)) { + sbject.add(EOSC_TWITTER); + } + return d; + }, Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath + "/dataset"); + + readPath(spark, workingPath + "/dataset", Dataset.class) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath + "/dataset"); + } + + private static boolean containscriteriaTwitter(Result r) { + Set words = getWordsSP(r.getTitle()); + words.addAll(getWordsF(r.getDescription())); + + if (words.contains("twitter") && + (words.contains("data") || words.contains("dataset"))) + return true; + + if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("twitter")) && + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("data"))) + return true; + return false; + } + + private static boolean containsCriteriaGalaxy(Result r) { + Set words = getWordsSP(r.getTitle()); + words.addAll(getWordsF(r.getDescription())); + if (words.contains("galaxy") && + words.contains("workflow")) + return true; + + if (r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("galaxy")) && + r.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("workflow"))) + return true; + return false; + } + + private static boolean containsCriteriaNotebook(Software s) { + if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("jupyter"))) + return true; + if (s + .getSubject() + .stream() + .anyMatch( + sbj -> sbj.getValue().toLowerCase().contains("python") && + sbj.getValue().toLowerCase().contains("notebook"))) + return true; + if (s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("python")) && + s.getSubject().stream().anyMatch(sbj -> sbj.getValue().toLowerCase().contains("notebook"))) + return true; + return false; + } + + private static Set getSubjects(List s) { + Set subjects = new HashSet<>(); + s.stream().forEach(sbj -> subjects.addAll(Arrays.asList(sbj.getValue().toLowerCase().split(" ")))); + s.stream().forEach(sbj -> subjects.add(sbj.getValue().toLowerCase())); + return subjects; + } + + private static Set getWordsSP(List elem) { + Set words = new HashSet<>(); + Optional + .ofNullable(elem) + .ifPresent( + e -> e + .forEach( + t -> words + .addAll( + Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); + return words; + } + + private static Set getWordsF(List> elem) { + Set words = new HashSet<>(); + Optional + .ofNullable(elem) + .ifPresent( + e -> e + .forEach( + t -> words + .addAll( + Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" "))))); +// elem +// .forEach( +// t -> words.addAll(Arrays.asList(t.getValue().toLowerCase().replaceAll("[^a-zA-Z ]", "").split(" ")))); + return words; + + } +} diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java index 42b7804ea..b9f3bff52 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/PrepareDatasourceCountryAssociation.java @@ -6,6 +6,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.Arrays; import java.util.List; +import java.util.Optional; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -87,6 +88,8 @@ public class PrepareDatasourceCountryAssociation { Dataset datasource = readPath(spark, inputPath + "/datasource", Datasource.class) .filter( (FilterFunction) ds -> !ds.getDataInfo().getDeletedbyinference() && + Optional.ofNullable(ds.getDatasourcetype()).isPresent() && + Optional.ofNullable(ds.getDatasourcetype().getClassid()).isPresent() && (allowedtypes.contains(ds.getDatasourcetype().getClassid()) || whitelist.contains(ds.getId()))); diff --git a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java index 56aa953b4..d9f6433a0 100644 --- a/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java +++ b/dhp-workflows/dhp-enrichment/src/main/java/eu/dnetlib/dhp/countrypropagation/SparkCountryPropagationJob.java @@ -102,21 +102,28 @@ public class SparkCountryPropagationJob { private static MapFunction, R> getCountryMergeFn() { return t -> { Optional.ofNullable(t._2()).ifPresent(r -> { - t._1().getCountry().addAll(merge(t._1().getCountry(), r.getCountrySet())); + if (Optional.ofNullable(t._1().getCountry()).isPresent()) + t._1().getCountry().addAll(merge(t._1().getCountry(), r.getCountrySet())); + else + t._1().setCountry(merge(null, t._2().getCountrySet())); }); return t._1(); }; } private static List merge(List c1, List c2) { - HashSet countries = c1 - .stream() - .map(Qualifier::getClassid) - .collect(Collectors.toCollection(HashSet::new)); + HashSet countries = new HashSet<>(); + if (Optional.ofNullable(c1).isPresent()) { + countries = c1 + .stream() + .map(Qualifier::getClassid) + .collect(Collectors.toCollection(HashSet::new)); + } + HashSet finalCountries = countries; return c2 .stream() - .filter(c -> !countries.contains(c.getClassid())) + .filter(c -> !finalCountries.contains(c.getClassid())) .map(c -> getCountry(c.getClassid(), c.getClassname())) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json new file mode 100644 index 000000000..4c25fea01 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/input_eoscTag_parameters.json @@ -0,0 +1,21 @@ +[ + { + "paramName":"s", + "paramLongName":"sourcePath", + "paramDescription": "the path of the sequencial file to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path used to store temporary output files", + "paramRequired": true + }, + { + "paramName": "ssm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "true if the spark session is managed, false otherwise", + "paramRequired": false + } + +] \ No newline at end of file diff --git a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml index f019f8413..f34c5110f 100644 --- a/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-enrichment/src/main/resources/eu/dnetlib/dhp/bulktag/oozie_app/workflow.xml @@ -204,7 +204,31 @@ - + + + + + yarn-cluster + cluster + EOSC_tagging + eu.dnetlib.dhp.bulktag.SparkEoscTag + dhp-enrichment-${projectVersion}.jar + + --num-executors=${sparkExecutorNumber} + --executor-memory=${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}${spark2EventLogDir} + + --sourcePath${outputPath} + --workingPath${workingDir}/eoscTag + + + + diff --git a/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java new file mode 100644 index 000000000..1ea254157 --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/java/eu/dnetlib/dhp/bulktag/EOSCTagJobTest.java @@ -0,0 +1,538 @@ + +package eu.dnetlib.dhp.bulktag; + +import static eu.dnetlib.dhp.bulktag.community.TaggingConstants.ZENODO_COMMUNITY_INDICATOR; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; + +import org.apache.commons.io.FileUtils; +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.Row; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.schema.oaf.*; + +public class EOSCTagJobTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(EOSCTagJobTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(EOSCTagJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(EOSCTagJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(EOSCTagJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + void jupyterUpdatesTest() throws Exception { + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/jupyter/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 4, + tmp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); + + Assertions + .assertEquals( + 1, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + + Assertions + .assertEquals( + 5, tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + + Assertions + .assertEquals( + 9, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + + Assertions + .assertEquals( + 5, tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::5aec1186054301b66c0c5dc35972a589")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + + Assertions + .assertEquals( + 9, tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::639909adfad9d708308f2aedb733e4a0")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + + List subjects = tmp + .filter(sw -> sw.getId().equals("50|od______1582::6e7a9b21a2feef45673890432af34244")) + .collect() + .get(0) + .getSubject(); + Assertions.assertEquals(8, subjects.size()); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("EOSC::Jupyter Notebook"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("jupyter"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("Modeling and Simulation"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("structure granulaire"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("algorithme"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("simulation numérique"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de gaz"))); + Assertions.assertTrue(subjects.stream().anyMatch(s -> s.getValue().equals("flux de liquide"))); + + Assertions + .assertEquals( + 10, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .count()); + + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)) + .filter( + ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); + + Assertions + .assertEquals( + 10, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .count()); + + Assertions + .assertEquals( + 0, sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)) + .filter( + ds -> ds.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Jupyter Notebook"))) + .count()); + + // spark.stop(); + } + + @Test + void galaxyUpdatesTest() throws Exception { + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/galaxy/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(11, tmp.count()); + + Assertions + .assertEquals( + 1, + tmp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) + .count()); + + Assertions + .assertEquals( + 2, tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::4132f5ec9496f0d6adc7b00a50a56ff4")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions + .assertEquals( + 5, tmp + .filter(sw -> sw.getId().equals("50|od______1582::501b25d420f808c8eddcd9b16e917f11")) + .collect() + .get(0) + .getSubject() + .size()); + + Assertions + .assertEquals( + 8, tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + tmp + .filter(sw -> sw.getId().equals("50|od______1582::581621232a561b7e8b4952b18b8b0e56")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + JavaRDD orp = sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + + Assertions.assertEquals(10, orp.count()); + + Assertions + .assertEquals( + 1, + orp + .filter( + s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Galaxy Workflow"))) + .count()); + + Assertions + .assertEquals( + 3, orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertTrue( + orp + .filter(sw -> sw.getId().equals("50|od______2017::0750a4d0782265873d669520f5e33c07")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions + .assertEquals( + 2, orp + .filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + orp + .filter(sw -> sw.getId().equals("50|od______2017::1bd97baef19dbd2db3203b112bb83bc5")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + Assertions + .assertEquals( + 2, orp + .filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")) + .collect() + .get(0) + .getSubject() + .size()); + Assertions + .assertFalse( + orp + .filter(sw -> sw.getId().equals("50|od______2017::1e400f1747487fd15998735c41a55c72")) + .collect() + .get(0) + .getSubject() + .stream() + .anyMatch(s -> s.getValue().equals("EOSC::Galaxy Workflow"))); + + } + + @Test + void twitterUpdatesTest() throws Exception { + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/software").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Software.class), + Encoders.bean(Software.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/software"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/dataset").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, Dataset.class), + Encoders.bean(Dataset.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/dataset"); + + spark + .read() + .textFile(getClass().getResource("/eu/dnetlib/dhp/eosctag/twitter/otherresearchproduct").getPath()) + .map( + (MapFunction) value -> OBJECT_MAPPER + .readValue(value, OtherResearchProduct.class), + Encoders.bean(OtherResearchProduct.class)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingDir.toString() + "/input/otherresearchproduct"); + + SparkEoscTag + .main( + new String[] { + "-isSparkSessionManaged", Boolean.FALSE.toString(), + "-sourcePath", + workingDir.toString() + "/input", + "-workingPath", workingDir.toString() + "/working" + + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/input/software") + .map(item -> OBJECT_MAPPER.readValue(item, Software.class)); + + Assertions.assertEquals(10, tmp.count()); + + Assertions + .assertEquals( + 0, + tmp + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + JavaRDD orp = sc + .textFile(workingDir.toString() + "/input/otherresearchproduct") + .map(item -> OBJECT_MAPPER.readValue(item, OtherResearchProduct.class)); + + Assertions.assertEquals(10, orp.count()); + + Assertions + .assertEquals( + 3, + orp + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + JavaRDD dats = sc + .textFile(workingDir.toString() + "/input/dataset") + .map(item -> OBJECT_MAPPER.readValue(item, Dataset.class)); + + Assertions.assertEquals(11, dats.count()); + + Assertions + .assertEquals( + 3, + dats + .filter(s -> s.getSubject().stream().anyMatch(sbj -> sbj.getValue().equals("EOSC::Twitter Data"))) + .count()); + + } +} diff --git a/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json new file mode 100644 index 000000000..645a7522f --- /dev/null +++ b/dhp-workflows/dhp-enrichment/src/test/resources/eu/dnetlib/dhp/eosctag/galaxy/dataset/dataset_10.json @@ -0,0 +1,10 @@ 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"galaxy framwork and software is itself aging, and achieving an adva an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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básico (1.º a 9.º anos), tendo como objetivo fornecer informação sobre as capacidades transversais que o novo Programa de Matemática português (2007) veio destacar.\nEscola Superior de Educação de 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in Europe","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"In the last decade, the number of centenarians world- wide has increased. Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Introduction: The number of centenarians has greatly increased in Portugal in the last decades. Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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the expected heterozygosity, or by R, the allelic richness). This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. Then compute the ratio of the two 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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se están desarrollando en la Universidad Camilo José Cela (UCJC) sobre la cafeína y sus efectos cuando se realiza deporte. https://www.ucjc.edu/2016/08/la-bbc-s...\n\nJuan Del Coso, director del Laboratorio de Fisiología del Ejercicio de la Universidad Camilo José Cela, nos describe cómo está siendo la investigación que desarrolla con deportistas de alto rendimiento y el consumo de cafeína.\n\n\"Nuestra investigación se enmarca dentro del campo de la fisiología del ejercicio y el objetivo que tenemos es investigar los efectos que tiene la cafeína en los deportistas, principalmente saber si es una ayuda ergogénica en la mayor parte de los deportes, pero también conocer qué perjuicios existen para aquellos deportistas que la utilizan para incrementar el rendimiento deportivo\", explica Del Coso.\n\nY es que los datos son muy llamativos: tres de cada cuatro deportistas de alto rendimiento utilizan la cafeína antes de la competición y muchas veces se utiliza sin saber los perjuicios que 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Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Quality of life","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Centenarians","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Centenarians´ quality of life and the role of health and living context","qualifier":{"classid":"main 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Oldest old","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Desportiva","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Metodologia","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Didática","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Treino 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básico (1.º a 9.º anos), tendo como objetivo fornecer informação sobre as capacidades transversais que o novo Programa de Matemática português (2007) veio destacar.\nEscola Superior de Educação de 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in Europe","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"In the last decade, the number of centenarians world- wide has increased. Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Introduction: The number of centenarians has greatly increased in Portugal in the last decades. Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this 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This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. 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El formato es al estilo inglés, similar al de la Oxford Union, donde algunos jóvenes se reunían a debatir sobre temas de la más candente actualidad y polemizaban con la intención de formarse en tan valoradas habilidades.\n\nLa Liga de Debate CICAE-UCJC es una ocasión única para los alumnos de ponerse en contacto con herramientas tan útiles como la oratoria y la comunicación efectiva. Pero, sobre todo, una oportunidad de fomentar el pensamiento crítico y la socialización entre alumnos con espíritu emprendedor. La Liga de Debate CICAE - Universidad Camilo José Cela se diferencia del resto de torneos en que potenciamos que sea eminentemente formativa. 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Estes agentes são responsáveis por perdas no rendimento que, normalmente, não são aceites pelo agricultor. E é, por isso, que se recorre aos pesticidas: é preciso proteger as culturas do ataque dos seus inimigos.\nTambém é verdade que a agricultura é a atividade desenvolvida pelo Homem que mais se aproxima dos sistemas naturais e tem, assim, um papel central na produção de diversos serviços do ecossistema, como a biodiversidade agrícola, qualidade do solo e água, estabilidade climática e manutenção da paisagem. Ora, o uso dos pesticidas introduz efeitos negativos em todo este sistema: degradam o solo, reduzem a qualidade e disponibilidade de água, causam poluição e perda de habitats selvagens e de biodiversidade. Aqui reside a encruzilhada na proteção das 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Evidences about their quality of life (QoL) are, nevertheless, still limited. Different conceptualizations of QoL, the overvaluation of the negative aspects of advanced age and the heterogeneity of the oldest old are some issues that could explain the dif􏰀culties in this assessment. Objectives: This study aims to analyze the perceived QoL in a sample of centenarians and analyze if there are significant life context (community vs institutional) and health (objective and subjective perception) differences.\nMethods: A subsample of 59 Portuguese centenarians who participated in the PT100_Oporto Centenarian Study, conducted in 2013 was considered. Descriptive and chi-square analysis were conducted.\nResults: Most centenarians perceived their QoL in a very positive manner (50.8% rated it as “good”, 6.8% as “very good” and 3.4% as “excellent”); 28.8% perceived it as “acceptable” and 10.2% as “bad”. No significant statistical differences were found for the considered variables.\nConclusions: Centenarians seem to present high levels of perceived QoL, which can be associated with a great ability to adapt to adverse situations that occur through their lives. Neither contextual and health aspects seem to in􏰂uence the perception of QoL in this particular sample study. Nonetheless, more research is \nneeded to understand the speci􏰀cities of the QoL in the centenarian population, namely the role of psychological and social variables.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[{"id":"http://zenodo.org/communities/edenis"},{"id":"http://zenodo.org/communities/aginfra"}, {"id":"http://zenodo.org/communities/primefish"}],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"instancetype":{"classid":"0020","classname":"Other ORP type","schemeid":"dnet:publication_resource","schemename":"dnet:publication_resource"},"hostedby":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"url":["http://hdl.handle.net/10400.19/5415"],"distributionlocation":"","collectedfrom":{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null},"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"processingchargeamount":null,"processingchargecurrency":null,"refereed":null}],"contactperson":[],"contactgroup":[],"tool":[]} +{"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1585055423836,"id":"50|od______2017::1e400f1747487fd15998735c41a55c72","originalId":["od______2017::1e400f1747487fd15998735c41a55c72"],"collectedfrom":[{"key":"opendoar____::2017","value":"Repositório Científico do Instituto Politécnico de Viseu","dataInfo":null}],"pid":[],"dateofcollection":"2019-02-25T04:30:56.996Z","dateoftransformation":"2019-11-30T04:19:59.556Z","extraInfo":[],"oaiprovenance":{"originDescription":{"harvestDate":"2019-02-25T04:30:56.996Z","altered":true,"baseURL":"http://repositorio.ipv.pt/oai/openaire","identifier":"oai:repositorio.ipv.pt:10400.19/5422","datestamp":"2019-02-23T03:01:29Z","metadataNamespace":"http://www.openarchives.org/OAI/2.0/oai_dc/"}},"author":[{"fullname":"Brandão, Daniela","name":"Daniela","surname":"Brandão","rank":1,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":2,"pid":null,"affiliation":null},{"fullname":"Araújo, Lia","name":"Lia","surname":"Araújo","rank":3,"pid":null,"affiliation":null},{"fullname":"Paul, Constança","name":"Constança","surname":"Paul","rank":4,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"TWITTER","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Census","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"What about the Portuguese oldest old? A global overview using census data","qualifier":{"classid":"main title","classname":"main title","schemeid":"dnet:dataCite_title","schemename":"dnet:dataCite_title"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"relevantdate":[],"description":[{"value":"Background\nThe older population is itself aging, and achieving an advanced age is becoming more common worldwide. In Portugal, individuals aged 80+ represent 5.6 % of the total population and 26.5 % of the popu- lation were aged 65 and over in 2011. Having a national profile on this population will give important information to develop interven- tion programs and identify the areas requiring most attention. Ob- jective: This study aims to provide a profile of the Portuguese oldest old, as given by the last national census data.\nMethods\nThe characteristics of all residents aged 80+ (N = 532,219) were ana- lysed considering socio-demographic information (gender, marital status, education, type of residence, place of birth, income) and the existence of difficulties in functional, sensorial and cognitive activities due to health problems or ageing.\nResults\nThe majority of the most aged are females (64.5 %), widowed (53.9 %), and present low educational levels (46.1 % never attended school and 31.6 % do not know how to read/write). Own pensions constitute the main source of income (96.3 %) and the majority live in private households (88.8 %), with 43.2 % currently living in the place where they were born. The majority (73.0 %) reported major difficulties in at least one functional activity – bathing/dressing, walk- ing/climbing stairs, seeing, hearing, memory/concentration, under- standing others/being understood.\nConclusions\nThe high percentage of oldest old living in private households and the presence of functional limitations point to the importance of in- formal care and community care services to support this population. Further studies paying attention to their needs and utilisation of ser- vices are 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Constança","name":"Constança","surname":"Paul","rank":5,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Twitter 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Following this tendency, the number of centenarian studies has also exponentially augmented. Given the complexity to conduct research with centenarians, elementary information on this specific age group remains unknown at a European level. This paper compares basic characteristics of centenarians from 32 European coun- tries based on Census 2011. Results revealed that France is the country with higher ratio of centenarians, followed by Italy and Greece; on the other hand Croatia, Romania and Bulgaria present the lower ratio. The distribution accord- ing to gender is similar for all countries, with higher ratio of women reaching 100 years old. Different patterns of education level were found on countries where this infor- mation was reliable: Portugal and Greece are the countries with lower levels of education, with more than half without formal education; Finland, UK and Iceland are the countries with higher levels of education, with all centenarians having at least lower secondary education. Analysing the residence situation (living in the community or living in the institu- tion), Romania, Bulgaria, Lithuania, Greece and Latvia are the countries that present higher percentages of centenarians living in the community; Iceland is the country with lower percentage of centenarians living in the community. A posi- tive correlation between the number of centenarians and the percentage of Total Health Expenditure of GDP is observed. This study provides important information about the current profile of European centenarians, which is compared to gen- eral information on the centenarian population from EUA and Asia.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2017-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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individuals aged 80 and over is growing faster than other segment of the population, and within this group the number of centenarians has risen exponentially worldwide. This phenomena lead to an increasing number of centenarian studies, improving the knowledge about this population, validating the idea of heterogeneity that char- acterizes this group. However, the factors influencing their aging survival remains understudied. The present study aims to identify factors associated with survival after 100 years old in a sample of Portuguese centenarians. After being included in a population-based study on centenarians (PT100–Oporto Centenarian Study), each participant was assessed by a tel- ephone interview every 6 months in order to assess his/her health condition. Follow-up was considered as the time (in months) between 100th birthday and death or the last tel- ephone contact. Survival analysis was performed to iden- tify factors associated with survival after 100 years old. Sociological and medical factors were considered. 140 cen- tenarians were assessed and 115 (82.1%) died. The median survival time after 100 years old was 38 months. Survival after age 100 was associated with acute disease (last month), self-perception of physical condition and drinking status. This study intends do identify factors that predict longevity in long-lived individuals. Findings recognize the importance of factors related with health status, self-perception of physi- cal condition and life style (no alcohol consume) for survival. Further studies should explore the predictive value of these factors, as well as psychosocial aspects, considering living longer but also the quality of time beyond one hundred.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2018-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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João","surname":"Azevedo","rank":5,"pid":null,"affiliation":null},{"fullname":"Ribeiro, Oscar","name":"Oscar","surname":"Ribeiro","rank":6,"pid":null,"affiliation":null}],"resulttype":{"classid":"other","classname":"other","schemeid":"dnet:result_typologies","schemename":"dnet:result_typologies"},"language":{"classid":"eng","classname":"English","schemeid":"dnet:languages","schemename":"dnet:languages"},"country":[],"subject":[{"value":"Cognition","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Survival","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},{"value":"Functional capacity","qualifier":{"classid":"keyword","classname":"keyword","schemeid":"dnet:result_subject","schemename":"dnet:result_subject"},"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"title":[{"value":"Cognition and functionality: how do they related to time lived after 100 years of age?","qualifier":{"classid":"main title","classname":"main 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Therefore, the analysis of survival time after becoming a centenarian and related factors constitute an import- ant issue for the quality of care provision. The objective of this study is to identify health related factors associated with the time lived after being 100 years of age. Methods: Data come from the population-based study PT100 (Oporto Centenarian Study) and considers information gathered through face-to-face interviews with centenarians and their proxies during 2013. Study eligibility criteria included being 100 and more years old and living in the Oporto Metropolitan Area. Survival analyses were performed in order to identify factors associated with survival after the 100. Functional status (e.g., walking, being bedrid- den) and specific health conditions (e.g. presence/absence of cognitive impairment) were considered as potential factors. Results: The sam- ple comprises 140 centenarians with approximately 14.5 months as median survival time after their 100th anniversary. Centenarians who were bedridden presented a higher probability to live after 100 years when compared with functionally independent centenarians. Presence of cognitive impairment was not associated with the time lived after 100 years old. Conclusions: Given the increasing number of centenarians in Portugal, different studies based on this population need to be consid- ered. The present study, focused on the life after 100 years old, provides new information about this topic contributing to the formulation of new scientific questions for this population.\ninfo:eu-repo/semantics/publishedVersion","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}}],"dateofacceptance":{"value":"2014-01-01","dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.9","inferenceprovenance":"","provenanceaction":{"classid":"sysimport:crosswalk:repository","classname":"sysimport:crosswalk:repository","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}}},"publisher":null,"embargoenddate":null,"source":[],"fulltext":[],"format":[],"contributor":[],"resourcetype":null,"coverage":[],"bestaccessright":null,"context":[],"externalReference":[],"instance":[{"license":null,"accessright":{"classid":"OPEN","classname":"Open 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This contribution is splitted in two components: one due to the diversity of the population, the other due to its differentiation from the remaining populations. The program may also be used to obtain allelic richness after rarefaction (to a sample size chosen by the investigator) for a set of populations. It can be used in conjunction with the program haplodiv, based on the paper by Pons & Petit 1995, TAG 90, 462-470, which will provide standard errors for the diversity and differentiation parameters. The input file is a text file (see example: rartest.txt), where the first line indicates the number of haplotypes (here it is 18), the number of populations (here it is 4), and the rarefaction size (it should not be larger than the smallest population sample size; here the rarefaction size is 10, and the smallest sample size is 20). Then follows the data for each population (line), with the number of each haplotype in each population (don't use relative frequencies): 18 4 10 1 0 1 0 0 0 1 1 ...(18 columns) 0 1 2 1 1 0 13 0 ... 0 0 8 0 0 3 6 0 ... 1 0 9 0 0 3 7 1 Results can be seen in the output file (rartest.out here; to be printed horizontally). General measures are given first: within population diversity (Hs), total diversity (Ht), and Gst are given, followed by similar measures based on allelic richness. Then you get the results for each population : H, its standard error, allelic richness after rarefaction, the divergence from the other populations (DHs, DHt, DGst, see the paper in Conservation Biology), and the contributions Ct, Cs, Cd followed by the contributions for allelic richness measures. The program is written for an haploid gene but may be used for nuclear genes, assuming Hardy-Weinberg equilibrium. How to proceed when there are several loci? Do not take the mean across Gst or across Contributions. They are ratios, so you should take the mean of the numerator and the mean of the denominator separately. For the denominator: take the mean of hT and Rt-1 across loci. For the numerator: multiply the contributions by hT or Rt-1 (respectively for contributions to diversity or to allelic richness) and take the mean of these products across loci. Then compute the ratio of the two 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into account the distances between haplotypes (ie, that consider all haplotypes equally divergent).[br/] The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of characters distinguishing the variants (for instance number of polymorphic fragments, or of polymorphic nucleotide sites). The program asks for the number of permutations to be made.[br/] see the example (\\ExamplePermut\\input.txt and \\ExamplePermut\\output.out).[br/] Then follows the number of individuals having a given cytotype (column) in a given population (row). Finally, and without interruption, provide the table of character states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Nst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Nst value is larger than the Gst, we count how many permutated values are larger than the observed Nst. If you have 5% of the permutated values greater than the observed value of Nst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Nst.[br/] [br/] README CpSSR :[br/] It computes measures of diversity and differenciation from haploid population genetic data, when the difference in number of repeats between alleles is available, and tests whether the differentiation and diversity measures differ from the equivalent measures when the distances between haplotypes is not considered (ie, when all haplotypes are considered equally divergent). The source file should be an ASCII file (its name should have 8 characters maximum: 12345678.txt) and should include the following information:[br/] First line :[br/] Number of cytotypes Number of populations Number of cpSSR loci. The program asks for the number of permutations to be made. See the example (\\ExampleCpSSR\\input.txt and \\ExamplePermut\\CpSSR.out).[br/] Then follows the number of individuals having a given haplotype (column) in a given population (row). Finally, and without interruption, provide the table of length variant states for all haplotypes, where each line corresponds to one haplotype, and each column to a character. No column should be empty (no missing haplotype) and each population (row) should be composed of AT LEAST 3 individuals![br/] The output file provides permutated values of Rst in a single row, and the value of the last 5% and last 1%. The mean of the permutated values is also given and should be close to the Gst value (by construction). To test if the observed Rst value is larger than the Gst, you count how many permutated values are larger than the observed Rst. If you have 5% of the permutated values greater than the observed value of Rst, then your test is not significant, otherwise it is and you know the P-value. This is akin to testing if Gst = Rst. 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+ +import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; + +import java.io.Serializable; +import java.util.List; +import java.util.Optional; +import java.util.stream.Collectors; + +import org.apache.commons.io.IOUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Dataset; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SaveMode; +import org.apache.spark.sql.SparkSession; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.application.ArgumentApplicationParser; +import eu.dnetlib.dhp.common.HdfsSupport; +import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.oaf.Context; +import eu.dnetlib.dhp.schema.oaf.Oaf; +import eu.dnetlib.dhp.schema.oaf.OafEntity; +import eu.dnetlib.dhp.schema.oaf.Result; +import eu.dnetlib.dhp.utils.ISLookupClientFactory; +import eu.dnetlib.enabling.is.lookup.rmi.ISLookUpService; + +public class CleanContextSparkJob implements Serializable { + private static final Logger log = LoggerFactory.getLogger(CleanContextSparkJob.class); + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + public static void main(String[] args) throws Exception { + + String jsonConfiguration = IOUtils + .toString( + CleanContextSparkJob.class + .getResourceAsStream( + "/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json")); + final ArgumentApplicationParser parser = new ArgumentApplicationParser(jsonConfiguration); + parser.parseArgument(args); + + Boolean isSparkSessionManaged = Optional + .ofNullable(parser.get("isSparkSessionManaged")) + .map(Boolean::valueOf) + .orElse(Boolean.TRUE); + log.info("isSparkSessionManaged: {}", isSparkSessionManaged); + + String inputPath = parser.get("inputPath"); + log.info("inputPath: {}", inputPath); + + String workingPath = parser.get("workingPath"); + log.info("workingPath: {}", workingPath); + + String contextId = parser.get("contextId"); + log.info("contextId: {}", contextId); + + String verifyParam = parser.get("verifyParam"); + log.info("verifyParam: {}", verifyParam); + + String graphTableClassName = parser.get("graphTableClassName"); + log.info("graphTableClassName: {}", graphTableClassName); + + Class entityClazz = (Class) Class.forName(graphTableClassName); + + SparkConf conf = new SparkConf(); + runWithSparkSession( + conf, + isSparkSessionManaged, + spark -> { + + cleanContext(spark, contextId, verifyParam, inputPath, entityClazz, workingPath); + }); + } + + private static void cleanContext(SparkSession spark, String contextId, String verifyParam, + String inputPath, Class entityClazz, String workingPath) { + Dataset res = spark + .read() + .textFile(inputPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)); + + res.map((MapFunction) r -> { + if (!r + .getTitle() + .stream() + .filter( + t -> t + .getQualifier() + .getClassid() + .equalsIgnoreCase(ModelConstants.MAIN_TITLE_QUALIFIER.getClassid())) + .anyMatch(t -> t.getValue().toLowerCase().startsWith(verifyParam.toLowerCase()))) { + return r; + } + r + .setContext( + r + .getContext() + .stream() + .filter( + c -> !c.getId().split("::")[0] + .equalsIgnoreCase(contextId)) + .collect(Collectors.toList())); + return r; + }, Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(workingPath); + + spark + .read() + .textFile(workingPath) + .map( + (MapFunction) value -> OBJECT_MAPPER.readValue(value, entityClazz), + Encoders.bean(entityClazz)) + .write() + .mode(SaveMode.Overwrite) + .option("compression", "gzip") + .json(inputPath); + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java index 474944260..5f2cd6808 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJob.java @@ -5,6 +5,7 @@ import static eu.dnetlib.dhp.common.SparkSessionSupport.runWithSparkSession; import java.util.*; import java.util.stream.Collectors; +import java.util.stream.Stream; import org.apache.commons.io.IOUtils; import org.apache.spark.SparkConf; @@ -136,7 +137,7 @@ public class MergeGraphTableSparkJob { /** * Datasources involved in the merge operation doesn't obey to the infra precedence policy, but relies on a custom * behaviour that, given two datasources from beta and prod returns the one from prod with the highest - * compatibility among the two. + * compatibility among the two. Furthermore, the procedure merges the collectedfrom, originalId, and pid lists. * * @param p datasource from PROD * @param b datasource from BETA @@ -160,9 +161,37 @@ public class MergeGraphTableSparkJob { List list = Arrays.asList(dp.getOpenairecompatibility(), db.getOpenairecompatibility()); dp.setOpenairecompatibility(Collections.min(list, new DatasourceCompatibilityComparator())); + dp + .setCollectedfrom( + Stream + .concat( + Optional + .ofNullable(dp.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty()), + Optional + .ofNullable(db.getCollectedfrom()) + .map(Collection::stream) + .orElse(Stream.empty())) + .distinct() // relies on KeyValue.equals + .collect(Collectors.toList())); + + dp.setOriginalId(mergeLists(dp.getOriginalId(), db.getOriginalId())); + dp.setPid(mergeLists(dp.getPid(), db.getPid())); + return (P) dp; } + private static final List mergeLists(final List... lists) { + return Arrays + .stream(lists) + .filter(Objects::nonNull) + .flatMap(List::stream) + .filter(Objects::nonNull) + .distinct() + .collect(Collectors.toList()); + } + private static

P mergeWithPriorityToPROD(Optional

p, Optional b) { if (b.isPresent() & !p.isPresent()) { return (P) b.get(); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java index 3e8ca1763..a05faab80 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/AbstractMdRecordToOafMapper.java @@ -18,14 +18,7 @@ import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.oaiIProvenance; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.qualifier; import static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.structuredProperty; -import java.util.ArrayList; -import java.util.Arrays; -import java.util.Date; -import java.util.HashMap; -import java.util.List; -import java.util.Map; -import java.util.Optional; -import java.util.Set; +import java.util.*; import org.apache.commons.lang3.StringUtils; import org.dom4j.*; @@ -35,6 +28,7 @@ import com.google.common.collect.Sets; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.common.ModelSupport; import eu.dnetlib.dhp.schema.oaf.AccessRight; import eu.dnetlib.dhp.schema.oaf.Author; import eu.dnetlib.dhp.schema.oaf.Context; @@ -199,8 +193,13 @@ public abstract class AbstractMdRecordToOafMapper { final List oafs = Lists.newArrayList(entity); if (!oafs.isEmpty()) { - oafs.addAll(addProjectRels(doc, entity)); - oafs.addAll(addOtherResultRels(doc, entity)); + Set rels = Sets.newHashSet(); + + rels.addAll(addProjectRels(doc, entity)); + rels.addAll(addOtherResultRels(doc, entity)); + rels.addAll(addRelations(doc, entity)); + + oafs.addAll(rels); } return oafs; @@ -278,6 +277,46 @@ public abstract class AbstractMdRecordToOafMapper { return res; } + private List addRelations(Document doc, OafEntity entity) { + + final List rels = Lists.newArrayList(); + + for (Object o : doc.selectNodes("//oaf:relation")) { + Element element = (Element) o; + + final String target = StringUtils.trim(element.getText()); + final String relType = element.attributeValue("relType"); + final String subRelType = element.attributeValue("subRelType"); + final String relClass = element.attributeValue("relClass"); + + if (StringUtils.isNotBlank(target) && StringUtils.isNotBlank(relType) && StringUtils.isNotBlank(subRelType) + && StringUtils.isNotBlank(relClass)) { + + final String relClassInverse = ModelSupport + .findInverse(ModelSupport.rel(relType, subRelType, relClass)) + .getInverseRelClass(); + final String validationdDate = ((Node) o).valueOf("@validationDate"); + + if (StringUtils.isNotBlank(target)) { + final String targetType = element.attributeValue("targetType"); + if (StringUtils.isNotBlank(targetType)) { + final String targetId = createOpenaireId(targetType, target, true); + rels + .add( + getRelation( + entity.getId(), targetId, relType, subRelType, relClass, entity, validationdDate)); + rels + .add( + getRelation( + targetId, entity.getId(), relType, subRelType, relClassInverse, entity, + validationdDate)); + } + } + } + } + return rels; + } + protected Relation getRelation(final String source, final String target, final String relType, @@ -340,7 +379,7 @@ public abstract class AbstractMdRecordToOafMapper { r.setPublisher(preparePublisher(doc, info)); r.setEmbargoenddate(prepareField(doc, "//oaf:embargoenddate", info)); r.setSource(prepareSources(doc, info)); - r.setFulltext(new ArrayList<>()); // NOT PRESENT IN MDSTORES + r.setFulltext(prepareListFields(doc, "//oaf:fulltext", info)); r.setFormat(prepareFormats(doc, info)); r.setContributor(prepareContributors(doc, info)); r.setResourcetype(prepareResourceType(doc, info)); diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java index 3e23e3493..63fa8b7e0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplication.java @@ -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.SOFTWARE_DEFAULT_RESULTTYPE; 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.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 static eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils.*; import java.io.Closeable; import java.io.IOException; @@ -143,8 +135,8 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i smdbe.execute("queryClaims.sql", smdbe::processClaims); break; case openaire: - log.info("Processing datasources..."); - smdbe.execute("queryDatasources.sql", smdbe::processDatasource, verifyNamespacePrefix); + log.info("Processing services..."); + smdbe.execute("queryServices.sql", smdbe::processService, verifyNamespacePrefix); log.info("Processing projects..."); if (dbSchema.equalsIgnoreCase("beta")) { @@ -156,10 +148,10 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i log.info("Processing Organizations..."); smdbe.execute("queryOrganizations.sql", smdbe::processOrganization, verifyNamespacePrefix); - log.info("Processing relationsNoRemoval ds <-> orgs ..."); + log.info("Processing relations services <-> orgs ..."); smdbe .execute( - "queryDatasourceOrganization.sql", smdbe::processDatasourceOrganization, + "queryServiceOrganization.sql", smdbe::processServiceOrganization, verifyNamespacePrefix); log.info("Processing projects <-> orgs ..."); @@ -235,32 +227,30 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i dbClient.processResults(sql, consumer); } - public List processDatasource(final ResultSet rs) { + public List processService(final ResultSet rs) { try { final DataInfo info = prepareDataInfo(rs); final Datasource ds = new Datasource(); - ds.setId(createOpenaireId(10, rs.getString("datasourceid"), true)); + ds.setId(createOpenaireId(10, rs.getString("id"), true)); ds .setOriginalId( Arrays - .asList((String[]) rs.getArray("identities").getArray()) + .asList((String[]) rs.getArray("originalid").getArray()) .stream() .filter(StringUtils::isNotBlank) .collect(Collectors.toList())); - ds - .setCollectedfrom( - listKeyValues( - createOpenaireId(10, rs.getString("collectedfromid"), true), - rs.getString("collectedfromname"))); - ds.setPid(new ArrayList<>()); + ds.setCollectedfrom(prepareCollectedfrom(rs.getArray("collectedfrom"))); + ds.setPid(prepareListOfStructProps(rs.getArray("pid"), info)); ds.setDateofcollection(asString(rs.getDate("dateofcollection"))); ds.setDateoftransformation(null); // Value not returned by the SQL query ds.setExtraInfo(new ArrayList<>()); // Values not present in the DB ds.setOaiprovenance(null); // Values not present in the DB ds.setDatasourcetype(prepareQualifierSplitting(rs.getString("datasourcetype"))); 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.setOfficialname(field(rs.getString("officialname"), 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.setOdpolicies(field(rs.getString("odpolicies"), 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.setReleasestartdate(field(asString(rs.getDate("releasestartdate")), info)); ds.setReleaseenddate(field(asString(rs.getDate("releaseenddate")), 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.setDatauploadtype(field(rs.getString("datauploadtype"), info)); ds.setDatabaseaccessrestriction(field(rs.getString("databaseaccessrestriction"), info)); ds.setDatauploadrestriction(field(rs.getString("datauploadrestriction"), info)); ds.setVersioning(field(rs.getBoolean("versioning"), info)); + ds.setVersioncontrol(rs.getBoolean("versioncontrol")); ds.setCitationguidelineurl(field(rs.getString("citationguidelineurl"), info)); - ds.setQualitymanagementkind(field(rs.getString("qualitymanagementkind"), info)); + ds.setPidsystems(field(rs.getString("pidsystems"), info)); ds.setCertificates(field(rs.getString("certificates"), info)); ds.setPolicies(new ArrayList<>()); // The sql query returns an empty array @@ -299,13 +288,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i journal( rs.getString("officialname"), rs.getString("issnPrinted"), rs.getString("issnOnline"), rs.getString("issnLinking"), info)); // Journal - ds.setDataInfo(info); - ds.setLastupdatetimestamp(lastUpdateTimestamp); + ds.setResearchentitytypes(listValues(rs.getArray("researchentitytypes"))); ds.setJurisdiction(prepareQualifierSplitting(rs.getString("jurisdiction"))); ds.setThematic(rs.getBoolean("thematic")); - ds.setKnowledgegraph(rs.getBoolean("knowledgegraph")); 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.setFulltextdownload(rs.getBoolean("fulltextdownload")); ds @@ -313,8 +307,18 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i Optional .ofNullable( rs.getDate("consenttermsofusedate")) - .map(c -> c.toString()) + .map(java.sql.Date::toString) .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); } catch (final Exception e) { @@ -425,11 +429,11 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i } } - public List processDatasourceOrganization(final ResultSet rs) { + public List processServiceOrganization(final ResultSet rs) { try { final DataInfo info = prepareDataInfo(rs); 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 collectedFrom = listKeyValues( createOpenaireId(10, rs.getString("collectedfromid"), true), rs.getString("collectedfromname")); @@ -603,6 +607,32 @@ public class MigrateDbEntitiesApplication extends AbstractMigrationApplication i String.format("%.3f", trust)); } + private List 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) { if (StringUtils.isBlank(s)) { return null; diff --git a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java index 6c72e4dfc..ab6f54b92 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java +++ b/dhp-workflows/dhp-graph-mapper/src/main/java/eu/dnetlib/dhp/oa/graph/raw/MigrateHdfsMdstoresApplication.java @@ -65,11 +65,19 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication log.info("isSparkSessionManaged: {}", isSparkSessionManaged); final String mdstoreManagerUrl = parser.get("mdstoreManagerUrl"); + log.info("mdstoreManagerUrl: {}", mdstoreManagerUrl); + final String mdFormat = parser.get("mdFormat"); + log.info("mdFormat: {}", mdFormat); + final String mdLayout = parser.get("mdLayout"); + log.info("mdLayout: {}", mdLayout); + final String mdInterpretation = parser.get("mdInterpretation"); + log.info("mdInterpretation: {}", mdInterpretation); final String hdfsPath = parser.get("hdfsPath"); + log.info("hdfsPath: {}", hdfsPath); final Set paths = mdstorePaths(mdstoreManagerUrl, mdFormat, mdLayout, mdInterpretation); @@ -95,6 +103,8 @@ public class MigrateHdfsMdstoresApplication extends AbstractMigrationApplication .filter(p -> HdfsSupport.exists(p, sc.hadoopConfiguration())) .toArray(size -> new String[size]); + log.info("Processing existing paths {}", Arrays.asList(validPaths)); + if (validPaths.length > 0) { spark .read() diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml index dc0529012..0cf6cdd05 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/clean/oozie_app/workflow.xml @@ -13,6 +13,23 @@ isLookupUrl the address of the lookUp service + + shouldCleanContext + true if the context have to be cleaned + + + contextId + sobigdata + It is the context id that should be removed from the result if the condition is matched. + Now it is just sobigdata. In a futere implementation I plan to have the contextId as value in a json + where to specify also the constraints that should be verified to remove the context from the result + + + verifyParam + gcube + It is the constrint to be verified. This time is hardcoded as gcube and it is searched for in + the title. If title starts with gcube than the context sobigdata will be removed by the result if present + sparkDriverMemory @@ -275,7 +292,131 @@ - + + + + + ${wf:conf('shouldCleanContext') eq true} + + + + + + + + + + + + + + yarn + cluster + Clean publications context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --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 + + --inputPath${graphOutputPath}/publication + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Publication + --workingPath${workingDir}/working/publication + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + + yarn + cluster + Clean datasets Context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/dataset + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Dataset + --workingPath${workingDir}/working/dataset + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + + yarn + cluster + Clean otherresearchproducts context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --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 + + --inputPath${graphOutputPath}/otherresearchproduct + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.OtherResearchProduct + --workingPath${workingDir}/working/otherresearchproduct + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + + + yarn + cluster + Clean softwares context + eu.dnetlib.dhp.oa.graph.clean.CleanContextSparkJob + dhp-graph-mapper-${projectVersion}.jar + + --executor-cores=${sparkExecutorCores} + --executor-memory=${sparkExecutorMemory} + --driver-memory=${sparkDriverMemory} + --conf spark.extraListeners=${spark2ExtraListeners} + --conf spark.sql.queryExecutionListeners=${spark2SqlQueryExecutionListeners} + --conf spark.yarn.historyServer.address=${spark2YarnHistoryServerAddress} + --conf spark.eventLog.dir=${nameNode}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --inputPath${graphOutputPath}/software + --graphTableClassNameeu.dnetlib.dhp.schema.oaf.Software + --workingPath${workingDir}/working/software + --contextId${contextId} + --verifyParam${verifyParam} + + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json new file mode 100644 index 000000000..e3d31d69f --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/input_clean_context_parameters.json @@ -0,0 +1,37 @@ +[ + { + "paramName": "issm", + "paramLongName": "isSparkSessionManaged", + "paramDescription": "when true will stop SparkSession after job execution", + "paramRequired": false + }, + { + "paramName": "in", + "paramLongName": "inputPath", + "paramDescription": "the path to the graph data dump to read", + "paramRequired": true + }, + { + "paramName": "wp", + "paramLongName": "workingPath", + "paramDescription": "the path to store the output graph", + "paramRequired": true + }, + { + "paramName": "ci", + "paramLongName": "contextId", + "paramDescription": "the id of the context to be removed", + "paramRequired": true + }, + { + "paramName": "class", + "paramLongName": "graphTableClassName", + "paramDescription": "class name moelling the graph table", + "paramRequired": true + },{ + "paramName": "vf", + "paramLongName": "verifyParam", + "paramDescription": "the parameter to be verified to remove the context", + "paramRequired": true +} +] diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml index 29d4269ef..31b726f39 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/raw_db/oozie_app/workflow.xml @@ -30,6 +30,11 @@ a blacklist of nsprefixes (comma separeted) + + reuseContent + false + reuse content in the aggregator database + sparkDriverMemory memory for driver process @@ -85,12 +90,20 @@ - + Action failed, error message[${wf:errorMessage(wf:lastErrorNode())}] + + + ${wf:conf('reuseContent') eq false} + ${wf:conf('reuseContent') eq true} + + + + @@ -102,6 +115,7 @@ --postgresUser${postgresUser} --postgresPassword${postgresPassword} --isLookupUrl${isLookupUrl} + --actionopenaire --dbschema${dbSchema} --nsPrefixBlacklist${nsPrefixBlacklist} @@ -124,6 +138,55 @@ --actionclaims --nsPrefixBlacklist${nsPrefixBlacklist} + + + + + + + yarn + cluster + GenerateEntities + eu.dnetlib.dhp.oa.graph.raw.GenerateEntitiesApplication + dhp-graph-mapper-${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}${spark2EventLogDir} + + --sourcePaths${contentPath}/db_records,${contentPath}/db_claims + --targetPath${workingDir}/entities + --isLookupUrl${isLookupUrl} + --shouldHashIdtrue + + + + + + + + yarn + cluster + GenerateGraph + eu.dnetlib.dhp.oa.graph.raw.DispatchEntitiesApplication + dhp-graph-mapper-${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}${spark2EventLogDir} + --conf spark.sql.shuffle.partitions=7680 + + --sourcePath${workingDir}/entities + --graphRawPath${workingDir}/graph_aggregator + diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql index 11a8c50af..3451333c0 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryOrganizations.sql @@ -27,7 +27,7 @@ SELECT 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, array_remove(array_agg(DISTINCT i.pid || '###' || i.issuertype || '@@@' || i.issuertype), NULL) AS pid 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_identities i ON (i.pid = p.pid) GROUP BY diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql index bcdef8221..d9a77427d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjectOrganization.sql @@ -16,4 +16,4 @@ SELECT FROM project_organization po LEFT OUTER JOIN projects p ON (p.id = po.project) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = p.collectedfrom); \ No newline at end of file + LEFT OUTER JOIN dsm_services dc ON (dc.id = p.collectedfrom); \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql index db0da83f7..af5913e75 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects.sql @@ -42,7 +42,7 @@ SELECT 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_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 fundingpaths fp ON (fp.id = pf.funding) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql index 234bb7c3e..80cbda4b7 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryProjects_production.sql @@ -40,7 +40,7 @@ SELECT 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_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 fundingpaths fp ON (fp.id = pf.funding) diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql similarity index 77% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql index f72e72105..02bed4b65 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasourceOrganization.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServiceOrganization.sql @@ -1,5 +1,5 @@ SELECT - dor.datasource AS datasource, + dor.service AS service, dor.organization AS organization, NULL AS startdate, NULL AS enddate, @@ -11,6 +11,6 @@ SELECT dc.officialname AS collectedfromname, 'providedBy@@@dnet:datasources_organizations_typologies' AS semantics, d.provenanceaction || '@@@dnet:provenanceActions' AS provenanceaction -FROM dsm_datasource_organization dor - LEFT OUTER JOIN dsm_datasources d ON (dor.datasource = d.id) - LEFT OUTER JOIN dsm_datasources dc ON (dc.id = d.collectedfrom); \ No newline at end of file +FROM dsm_service_organization dor + LEFT OUTER JOIN dsm_services d ON (dor.service = d.id) + LEFT OUTER JOIN dsm_services dc ON (dc.id = d.collectedfrom); \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql similarity index 60% rename from dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql rename to dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql index 2623c65c4..c4096f90d 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryDatasources.sql +++ b/dhp-workflows/dhp-graph-mapper/src/main/resources/eu/dnetlib/dhp/oa/graph/sql/queryServices.sql @@ -1,6 +1,7 @@ SELECT - d.id AS datasourceid, - d.id || array_agg(distinct di.pid) AS identities, + d.id AS id, + 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.englishname AS englishname, d.contactemail AS contactemail, @@ -9,8 +10,8 @@ SELECT THEN 'openaire-cris_1.1@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['openaire4.0']) - THEN - 'openaire4.0@@@dnet:datasourceCompatibilityLevel' + THEN + 'openaire4.0@@@dnet:datasourceCompatibilityLevel' WHEN (array_agg(DISTINCT COALESCE (a.compatibility_override, a.compatibility):: TEXT) @> ARRAY ['driver', 'openaire2.0']) THEN 'driver-openaire2.0@@@dnet:datasourceCompatibilityLevel' @@ -40,25 +41,29 @@ SELECT END AS openairecompatibility, d.websiteurl AS websiteurl, 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.longitude AS longitude, d.namespaceprefix AS namespaceprefix, NULL AS odnumberofitems, NULL AS odnumberofitemsdate, - - (SELECT array_agg(s|| '###keywords@@@dnet:subject_classification_typologies') + (SELECT array_agg(s|| '###keyword@@@dnet:subject_classification_typologies') FROM UNNEST( ARRAY( 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, NULL AS odpolicies, - ARRAY(SELECT trim(s) - FROM unnest(string_to_array(d.languages, ',')) AS s) AS odlanguages, - ARRAY(SELECT trim(s) - FROM unnest(string_to_array(d.od_contenttypes, '-')) AS s) AS odcontenttypes, + array_remove(ARRAY(SELECT trim(s) + FROM unnest(string_to_array(regexp_replace(d.languages, '{|}|"', '', 'g'), ',')) AS s), '{}') AS odlanguages, + array_remove(ARRAY(SELECT trim(s) + 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 deletedbyinference, 0.9 AS trust, @@ -69,39 +74,59 @@ SELECT d.releasestartdate AS releasestartdate, d.releaseenddate AS releaseenddate, d.missionstatementurl AS missionstatementurl, - d.dataprovider AS dataprovider, - d.serviceprovider AS serviceprovider, + -- the following 2 fields (provided by re3data) have been replaced by research_entity_types[] + -- VALUE 'Research Data' : d.dataprovider AS dataprovider, + -- VALUE 'Services' : d.serviceprovider AS serviceprovider, d.databaseaccesstype AS databaseaccesstype, d.datauploadtype AS datauploadtype, d.databaseaccessrestriction AS databaseaccessrestriction, 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.qualitymanagementkind AS qualitymanagementkind, - d.pidsystems AS pidsystems, + array_to_string(array_agg(distinct dps.scheme), ' ') AS pidsystems, d.certificates AS certificates, ARRAY[]::text[] AS policies, - dc.id AS collectedfromid, - dc.officialname AS collectedfromname, - d.typology||'@@@dnet:datasource_typologies' AS datasourcetype, - d.typology||'@@@dnet:datasource_typologies_ui' AS datasourcetypeui, - 'sysimport:crosswalk:entityregistry@@@dnet:provenance_actions' AS provenanceaction, + array_remove( + array( + select distinct cf + from unnest( + 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.eissn AS issnOnline, d.lissn AS issnLinking, + d.research_entity_types AS researchentitytypes, d.consenttermsofuse AS consenttermsofuse, d.fulltextdownload AS fulltextdownload, d.consenttermsofusedate AS consenttermsofusedate, - de.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, - de.thematic AS thematic, - de.knowledge_graph AS knowledgegraph, - array(select unnest(de.content_policies)||'@@@eosc:contentpolicies') AS contentpolicies + d.lastconsenttermsofusedate AS lastconsenttermsofusedate, + d.jurisdiction||'@@@eosc:jurisdictions' AS jurisdiction, + d.thematic AS thematic, + 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 -LEFT OUTER JOIN dsm_datasources_eosc de on (d.id = de.id) -LEFT OUTER JOIN dsm_datasources dc on (d.collectedfrom = dc.id) -LEFT OUTER JOIN dsm_api a ON (d.id = a.datasource) -LEFT OUTER JOIN dsm_datasourcepids di ON (d.id = di.datasource) +FROM dsm_services d +LEFT OUTER JOIN dsm_services dc on (d.collectedfrom = dc.id) +LEFT OUTER JOIN dsm_api a ON (d.id = a.service) +LEFT OUTER JOIN dsm_servicepids dp ON (d.id = dp.service) +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 d.id, @@ -119,23 +144,27 @@ GROUP BY d.releasestartdate, d.releaseenddate, d.missionstatementurl, - d.dataprovider, - d.serviceprovider, + -- TODO REMOVED ???: d.dataprovider, + -- TODO REMOVED ???: d.serviceprovider, d.databaseaccesstype, d.datauploadtype, d.databaseaccessrestriction, d.datauploadrestriction, - d.versioning, + -- REPLACED BY version_control : d.versioning, + d.version_control, d.citationguidelineurl, - d.qualitymanagementkind, - d.pidsystems, + -- REMOVED: d.qualitymanagementkind, d.certificates, dc.id, dc.officialname, d.issn, d.eissn, d.lissn, - de.jurisdiction, - de.thematic, - de.knowledge_graph, - de.content_policies + d.jurisdiction, + d.thematic, + -- REMOVED ???: de.knowledge_graph, + d.content_policies, + d.submission_policy_url, + d.preservation_policy_url, + d.research_product_access_policies, + d.research_product_metadata_access_policies \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala index f13c14da5..bd970a5cf 100644 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala +++ b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/SparkConvertRDDtoDataset.scala @@ -7,6 +7,7 @@ import org.apache.commons.io.IOUtils import org.apache.spark.SparkConf import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} import org.slf4j.{Logger, LoggerFactory} +import scala.collection.JavaConverters._ object SparkConvertRDDtoDataset { @@ -94,8 +95,8 @@ object SparkConvertRDDtoDataset { log.info("Converting Relation") val relationSemanticFilter = List( - "cites", - "iscitedby", +// "cites", +// "iscitedby", "merges", "ismergedin", "HasAmongTopNSimilarDocuments", @@ -107,6 +108,12 @@ object SparkConvertRDDtoDataset { .map(s => mapper.readValue(s, classOf[Relation])) .filter(r => r.getDataInfo != null && r.getDataInfo.getDeletedbyinference == false) .filter(r => r.getSource.startsWith("50") && r.getTarget.startsWith("50")) + //filter OpenCitations relations + .filter(r => + r.getCollectedfrom != null && r.getCollectedfrom.size() > 0 && !r.getCollectedfrom.asScala.exists(k => + "opencitations".equalsIgnoreCase(k.getValue) + ) + ) .filter(r => !relationSemanticFilter.exists(k => k.equalsIgnoreCase(r.getRelClass))) spark.createDataset(rddRelation).as[Relation].write.mode(SaveMode.Overwrite).save(s"$relPath") diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala deleted file mode 100644 index 23f4da6c7..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/PangaeaUtils.scala +++ /dev/null @@ -1,136 +0,0 @@ -package eu.dnetlib.dhp.sx.graph.pangaea - -import org.apache.spark.sql.expressions.Aggregator -import org.apache.spark.sql.{Encoder, Encoders} -import org.json4s -import org.json4s.DefaultFormats -import org.json4s.jackson.JsonMethods.parse - -import java.util.regex.Pattern -import scala.language.postfixOps -import scala.xml.{Elem, Node, XML} - -case class PangaeaDataModel( - identifier: String, - title: List[String], - objectType: List[String], - creator: List[String], - publisher: List[String], - dataCenter: List[String], - subject: List[String], - language: String, - rights: String, - parent: String, - relation: List[String], - linkage: List[(String, String)] -) {} - -object PangaeaUtils { - - def toDataset(input: String): PangaeaDataModel = { - implicit lazy val formats: DefaultFormats.type = org.json4s.DefaultFormats - lazy val json: json4s.JValue = parse(input) - val xml = (json \ "xml").extract[String] - parseXml(xml) - } - - def findDOIInRelation(input: List[String]): List[String] = { - val pattern = Pattern.compile("\\b(10[.][0-9]{4,}(?:[.][0-9]+)*\\/(?:(?![\"&\\'<>])\\S)+)\\b") - input - .map(i => { - val matcher = pattern.matcher(i) - if (matcher.find()) - matcher.group(0) - else - null - }) - .filter(i => i != null) - } - - def attributeOpt(attribute: String, node: Node): Option[String] = - node.attribute(attribute) flatMap (_.headOption) map (_.text) - - def extractLinkage(node: Elem): List[(String, String)] = { - (node \ "linkage") - .map(n => (attributeOpt("type", n), n.text)) - .filter(t => t._1.isDefined) - .map(t => (t._1.get, t._2))(collection.breakOut) - } - - def parseXml(input: String): PangaeaDataModel = { - val xml = XML.loadString(input) - - val identifier = (xml \ "identifier").text - val title: List[String] = (xml \ "title").map(n => n.text)(collection.breakOut) - val pType: List[String] = (xml \ "type").map(n => n.text)(collection.breakOut) - val creators: List[String] = (xml \ "creator").map(n => n.text)(collection.breakOut) - val publisher: List[String] = (xml \ "publisher").map(n => n.text)(collection.breakOut) - val dataCenter: List[String] = (xml \ "dataCenter").map(n => n.text)(collection.breakOut) - val subject: List[String] = (xml \ "subject").map(n => n.text)(collection.breakOut) - val language = (xml \ "language").text - val rights = (xml \ "rights").text - val parentIdentifier = (xml \ "parentIdentifier").text - val relation: List[String] = (xml \ "relation").map(n => n.text)(collection.breakOut) - val relationFiltered = findDOIInRelation(relation) - val linkage: List[(String, String)] = extractLinkage(xml) - - PangaeaDataModel( - identifier, - title, - pType, - creators, - publisher, - dataCenter, - subject, - language, - rights, - parentIdentifier, - relationFiltered, - linkage - ) - } - - def getDatasetAggregator(): Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel] = - new Aggregator[(String, PangaeaDataModel), PangaeaDataModel, PangaeaDataModel] { - - override def zero: PangaeaDataModel = null - - override def reduce(b: PangaeaDataModel, a: (String, PangaeaDataModel)): PangaeaDataModel = { - if (b == null) - a._2 - else { - if (a == null) - b - else { - if (b.title != null && b.title.nonEmpty) - b - else - a._2 - - } - } - } - - override def merge(b1: PangaeaDataModel, b2: PangaeaDataModel): PangaeaDataModel = { - if (b1 == null) - b2 - else { - if (b2 == null) - b1 - else { - if (b1.title != null && b1.title.nonEmpty) - b1 - else - b2 - - } - } - } - override def finish(reduction: PangaeaDataModel): PangaeaDataModel = reduction - - override def bufferEncoder: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel] - - override def outputEncoder: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel] - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala b/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala deleted file mode 100644 index 8ff8a8b1a..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/main/scala/eu/dnetlib/dhp/sx/graph/pangaea/SparkGeneratePanagaeaDataset.scala +++ /dev/null @@ -1,58 +0,0 @@ -package eu.dnetlib.dhp.sx.graph.pangaea - -import eu.dnetlib.dhp.application.ArgumentApplicationParser -import org.apache.spark.rdd.RDD -import org.apache.spark.sql.{Encoder, Encoders, SaveMode, SparkSession} -import org.apache.spark.{SparkConf, SparkContext} -import org.slf4j.{Logger, LoggerFactory} -import scala.collection.JavaConverters._ - -import scala.io.Source - -object SparkGeneratePanagaeaDataset { - - def main(args: Array[String]): Unit = { - val logger: Logger = LoggerFactory.getLogger(getClass) - val conf: SparkConf = new SparkConf() - val parser = new ArgumentApplicationParser( - Source - .fromInputStream( - getClass.getResourceAsStream("/eu/dnetlib/dhp/sx/pangaea/pangaea_to_dataset.json") - ) - .mkString - ) - parser.parseArgument(args) - - val spark: SparkSession = - SparkSession - .builder() - .config(conf) - .appName(SparkGeneratePanagaeaDataset.getClass.getSimpleName) - .master(parser.get("master")) - .getOrCreate() - - parser.getObjectMap.asScala.foreach(s => logger.info(s"${s._1} -> ${s._2}")) - logger.info("Converting sequential file into Dataset") - val sc: SparkContext = spark.sparkContext - - val workingPath: String = parser.get("workingPath") - - implicit val pangaeaEncoders: Encoder[PangaeaDataModel] = Encoders.kryo[PangaeaDataModel] - - val inputRDD: RDD[PangaeaDataModel] = - sc.textFile(s"$workingPath/update").map(s => PangaeaUtils.toDataset(s)) - - spark - .createDataset(inputRDD) - .as[PangaeaDataModel] - .map(s => (s.identifier, s))(Encoders.tuple(Encoders.STRING, pangaeaEncoders)) - .groupByKey(_._1)(Encoders.STRING) - .agg(PangaeaUtils.getDatasetAggregator().toColumn) - .map(s => s._2) - .write - .mode(SaveMode.Overwrite) - .save(s"$workingPath/dataset") - - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java new file mode 100644 index 000000000..472d3781d --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/CleanContextTest.java @@ -0,0 +1,300 @@ + +package eu.dnetlib.dhp.oa.graph.clean; + +import java.io.IOException; +import java.nio.file.Files; +import java.nio.file.Path; +import java.util.List; +import java.util.Locale; + +import org.apache.commons.io.FileUtils; +import org.apache.spark.SparkConf; +import org.apache.spark.api.java.JavaRDD; +import org.apache.spark.api.java.JavaSparkContext; +import org.apache.spark.api.java.function.MapFunction; +import org.apache.spark.sql.Encoders; +import org.apache.spark.sql.SparkSession; +import org.junit.jupiter.api.AfterAll; +import org.junit.jupiter.api.Assertions; +import org.junit.jupiter.api.BeforeAll; +import org.junit.jupiter.api.Test; +import org.slf4j.Logger; +import org.slf4j.LoggerFactory; + +import com.fasterxml.jackson.core.JsonProcessingException; +import com.fasterxml.jackson.databind.ObjectMapper; + +import eu.dnetlib.dhp.oa.graph.dump.Constants; +import eu.dnetlib.dhp.oa.graph.dump.DumpJobTest; +import eu.dnetlib.dhp.oa.graph.dump.DumpProducts; +import eu.dnetlib.dhp.oa.graph.dump.community.CommunityMap; +import eu.dnetlib.dhp.schema.common.ModelConstants; +import eu.dnetlib.dhp.schema.dump.oaf.Instance; +import eu.dnetlib.dhp.schema.dump.oaf.OpenAccessRoute; +import eu.dnetlib.dhp.schema.dump.oaf.graph.GraphResult; +import eu.dnetlib.dhp.schema.oaf.Publication; +import eu.dnetlib.dhp.schema.oaf.Software; +import eu.dnetlib.dhp.schema.oaf.StructuredProperty; + +public class CleanContextTest { + + private static final ObjectMapper OBJECT_MAPPER = new ObjectMapper(); + + private static SparkSession spark; + + private static Path workingDir; + + private static final Logger log = LoggerFactory.getLogger(CleanContextTest.class); + + @BeforeAll + public static void beforeAll() throws IOException { + workingDir = Files.createTempDirectory(DumpJobTest.class.getSimpleName()); + log.info("using work dir {}", workingDir); + + SparkConf conf = new SparkConf(); + conf.setAppName(DumpJobTest.class.getSimpleName()); + + conf.setMaster("local[*]"); + conf.set("spark.driver.host", "localhost"); + conf.set("hive.metastore.local", "true"); + conf.set("spark.ui.enabled", "false"); + conf.set("spark.sql.warehouse.dir", workingDir.toString()); + conf.set("hive.metastore.warehouse.dir", workingDir.resolve("warehouse").toString()); + + spark = SparkSession + .builder() + .appName(DumpJobTest.class.getSimpleName()) + .config(conf) + .getOrCreate(); + } + + @AfterAll + public static void afterAll() throws IOException { + FileUtils.deleteDirectory(workingDir.toFile()); + spark.stop(); + } + + @Test + public void testResultClean() throws Exception { + final String sourcePath = getClass() + .getResource("/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json") + .getPath(); + final String prefix = "gcube "; + + spark + .read() + .textFile(sourcePath) + .map( + (MapFunction) r -> OBJECT_MAPPER.readValue(r, Publication.class), + Encoders.bean(Publication.class)) + .write() + .json(workingDir.toString() + "/publication"); + + CleanContextSparkJob.main(new String[] { + "--isSparkSessionManaged", Boolean.FALSE.toString(), + "--inputPath", workingDir.toString() + "/publication", + "-graphTableClassName", Publication.class.getCanonicalName(), + "-workingPath", workingDir.toString() + "/working", + "-contextId", "sobigdata", + "-verifyParam", "gCube " + }); + + final JavaSparkContext sc = JavaSparkContext.fromSparkContext(spark.sparkContext()); + JavaRDD tmp = sc + .textFile(workingDir.toString() + "/publication") + .map(item -> OBJECT_MAPPER.readValue(item, Publication.class)); + + Assertions.assertEquals(7, tmp.count()); + + // original result with sobigdata context and gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 0, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::0224aae28af558f21768dbc6439c7a95")) + .collect() + .get(0) + .getContext() + .size()); + + // original result with sobigdata context without gcube as starting string in the main title for the publication + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::20c414a3b1c742d5dd3851f1b67df2d9")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + + // original result with sobigdata context with gcube as starting string in the subtitle + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::2", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + List titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c81248c335f0aa07e06817ece6fa6af")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("subtitle", titles.get(0).getQualifier().getClassid()); + + // original result with sobigdata context with gcube not as starting string in the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "sobigdata::projects::1", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::3c9f068ddc930360bec6925488a9a97f")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertFalse(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().contains(prefix.trim())); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + // original result with sobigdata in context and also other contexts with gcube as starting string for the main + // title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4669a378a73661417182c208e6fdab53")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(1, titles.size()); + Assertions.assertTrue(titles.get(0).getValue().toLowerCase().startsWith(prefix)); + Assertions.assertEquals("main title", titles.get(0).getQualifier().getClassid()); + + // original result with multiple main title one of which whith gcube as starting string and with 2 contextes + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|DansKnawCris::4a9152e80f860eab99072e921d74a0ff")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); + + // original result without sobigdata in context with gcube as starting string for the main title + Assertions + .assertEquals( + 1, + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .size()); + Assertions + .assertEquals( + "dh-ch", + tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getContext() + .get(0) + .getId()); + titles = tmp + .filter(p -> p.getId().equals("50|dedup_wf_001::01e6a28565ca01376b7548e530c6f6e8")) + .collect() + .get(0) + .getTitle(); + Assertions.assertEquals(2, titles.size()); + + Assertions + .assertTrue( + titles + .stream() + .anyMatch( + t -> t.getQualifier().getClassid().equals("main title") + && t.getValue().toLowerCase().startsWith(prefix))); + + } +} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJobTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJobTest.java index 2d28ee305..7dcb4bca4 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJobTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/merge/MergeGraphTableSparkJobTest.java @@ -2,6 +2,7 @@ package eu.dnetlib.dhp.oa.graph.merge; import static org.junit.jupiter.api.Assertions.assertEquals; +import static org.junit.jupiter.api.Assertions.assertNotNull; import java.io.IOException; import java.util.Optional; @@ -25,7 +26,23 @@ class MergeGraphTableSparkJobTest { } @Test - void testMergeDatasources() throws IOException { + void testMerge() throws IOException { + Datasource d = MergeGraphTableSparkJob + .mergeDatasource( + d("datasource_cris.json"), + d("datasource_openaire2.0.json")); + + assertEquals("10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", d.getId()); + assertNotNull(d.getOriginalId()); + assertEquals(2, d.getOriginalId().size()); + assertNotNull(d.getCollectedfrom()); + assertEquals(2, d.getCollectedfrom().size()); + assertNotNull(d.getPid()); + assertEquals(1, d.getPid().size()); + } + + @Test + void testMergeCompatibility() throws IOException { assertEquals( "openaire-cris_1.1", MergeGraphTableSparkJob 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 bdb73abf5..b75f626d6 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 @@ -57,14 +57,10 @@ class MappersTest { final List list = new OafToOafMapper(vocs, false, true).processMdRecord(xml); - assertEquals(3, list.size()); - assertTrue(list.get(0) instanceof Publication); - assertTrue(list.get(1) instanceof Relation); - assertTrue(list.get(2) instanceof Relation); + assertEquals(1, list.stream().filter(o -> o instanceof Publication).count()); + assertEquals(4, list.stream().filter(o -> o instanceof Relation).count()); - final Publication p = (Publication) list.get(0); - final Relation r1 = (Relation) list.get(1); - final Relation r2 = (Relation) list.get(2); + Publication p = (Publication) list.stream().filter(o -> o instanceof Publication).findFirst().get(); assertValidId(p.getId()); @@ -125,26 +121,62 @@ class MappersTest { assertNotNull(p.getBestaccessright()); assertEquals("OPEN", p.getBestaccessright().getClassid()); - assertValidId(r1.getSource()); - assertValidId(r1.getTarget()); - assertValidId(r2.getSource()); - assertValidId(r2.getTarget()); - assertValidId(r1.getCollectedfrom().get(0).getKey()); - assertValidId(r2.getCollectedfrom().get(0).getKey()); - assertNotNull(r1.getDataInfo()); - assertNotNull(r2.getDataInfo()); - assertNotNull(r1.getDataInfo().getTrust()); - assertNotNull(r2.getDataInfo().getTrust()); - assertEquals(r1.getSource(), r2.getTarget()); - assertEquals(r2.getSource(), r1.getTarget()); - assertTrue(StringUtils.isNotBlank(r1.getRelClass())); - assertTrue(StringUtils.isNotBlank(r2.getRelClass())); - assertTrue(StringUtils.isNotBlank(r1.getRelType())); - assertTrue(StringUtils.isNotBlank(r2.getRelType())); - assertTrue(r1.getValidated()); - assertTrue(r2.getValidated()); - assertEquals("2020-01-01", r1.getValidationDate()); - assertEquals("2020-01-01", r2.getValidationDate()); + + assertNotNull(p.getFulltext()); + assertEquals(1, p.getFulltext().size()); + assertEquals("https://oneecosystem.pensoft.net/article/13718/", p.getFulltext().get(0).getValue()); + + // RESULT PROJECT + List resultProject = list + .stream() + .filter(o -> o instanceof Relation) + .map(o -> (Relation) o) + .filter(r -> ModelConstants.RESULT_PROJECT.equals(r.getRelType())) + .collect(Collectors.toList()); + + assertEquals(2, resultProject.size()); + final Relation rp1 = resultProject.get(0); + final Relation rp2 = resultProject.get(1); + + verifyRelation(rp1); + verifyRelation(rp2); + + assertTrue(rp1.getValidated()); + assertTrue(rp2.getValidated()); + assertEquals("2020-01-01", rp1.getValidationDate()); + assertEquals("2020-01-01", rp2.getValidationDate()); + + assertEquals(rp1.getSource(), rp2.getTarget()); + assertEquals(rp2.getSource(), rp1.getTarget()); + + // AFFILIATIONS + List affiliation = list + .stream() + .filter(o -> o instanceof Relation) + .map(o -> (Relation) o) + .filter(r -> ModelConstants.RESULT_ORGANIZATION.equals(r.getRelType())) + .collect(Collectors.toList()); + + assertEquals(2, affiliation.size()); + final Relation aff1 = affiliation.get(0); + final Relation aff2 = affiliation.get(1); + + verifyRelation(aff1); + verifyRelation(aff2); + + assertEquals(aff1.getSource(), aff2.getTarget()); + assertEquals(aff2.getSource(), aff1.getTarget()); + } + + private void verifyRelation(Relation r) { + assertValidId(r.getSource()); + assertValidId(r.getTarget()); + assertValidId(r.getCollectedfrom().get(0).getKey()); + assertNotNull(r.getDataInfo()); + assertNotNull(r.getDataInfo().getTrust()); + assertTrue(StringUtils.isNotBlank(r.getRelClass())); + assertTrue(StringUtils.isNotBlank(r.getRelType())); + } @Test @@ -734,6 +766,51 @@ class MappersTest { assertFalse(p_cleaned.getTitle().isEmpty()); } + @Test + void testZenodo() throws IOException, DocumentException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("odf_zenodo.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); + + final Publication p = (Publication) list.get(0); + assertValidId(p.getId()); + assertValidId(p.getCollectedfrom().get(0).getKey()); + + assertNotNull(p.getTitle()); + assertFalse(p.getTitle().isEmpty()); + assertEquals(1, p.getTitle().size()); + assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + + assertNotNull(p.getAuthor()); + assertEquals(2, p.getAuthor().size()); + + Author author = p + .getAuthor() + .stream() + .filter(a -> a.getPid().stream().anyMatch(pi -> pi.getValue().equals("0000-0003-3272-8007"))) + .findFirst() + .get(); + assertNotNull(author); + assertTrue(StringUtils.isBlank(author.getSurname())); + assertTrue(StringUtils.isBlank(author.getName())); + assertEquals("Anne van Weerden", author.getFullname()); + + author = p + .getAuthor() + .stream() + .filter(a -> a.getPid().stream().anyMatch(pi -> pi.getValue().equals("0000-0003-3272-8008"))) + .findFirst() + .get(); + assertNotNull(author); + assertFalse(StringUtils.isBlank(author.getSurname())); + assertFalse(StringUtils.isBlank(author.getName())); + assertFalse(StringUtils.isBlank(author.getFullname())); + + } + @Test void testOdfFromHdfs() throws IOException, DocumentException { final String xml = IOUtils @@ -835,6 +912,20 @@ class MappersTest { assertEquals("EUR", p.getProcessingchargecurrency().getValue()); } + @Test + void testROHub() throws IOException, DocumentException { + final String xml = IOUtils.toString(Objects.requireNonNull(getClass().getResourceAsStream("rohub.xml"))); + final List list = new OdfToOafMapper(vocs, false, true).processMdRecord(xml); + System.out.println("***************"); + System.out.println(new ObjectMapper().writeValueAsString(list)); + System.out.println("***************"); +// final Dataset p = (Dataset) list.get(0); +// assertValidId(p.getId()); +// assertValidId(p.getCollectedfrom().get(0).getKey()); +// System.out.println(p.getTitle().get(0).getValue()); +// assertTrue(StringUtils.isNotBlank(p.getTitle().get(0).getValue())); + } + private void assertValidId(final String id) { // System.out.println(id); diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java index 05ae5be74..9048a22ea 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java +++ b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/raw/MigrateDbEntitiesApplicationTest.java @@ -12,8 +12,11 @@ import java.sql.Array; import java.sql.Date; import java.sql.ResultSet; import java.sql.SQLException; +import java.util.HashSet; import java.util.List; import java.util.Objects; +import java.util.Optional; +import java.util.stream.Collectors; import org.apache.commons.io.IOUtils; import org.apache.commons.lang3.StringUtils; @@ -28,12 +31,7 @@ import com.fasterxml.jackson.core.type.TypeReference; import com.fasterxml.jackson.databind.ObjectMapper; import eu.dnetlib.dhp.common.vocabulary.VocabularyGroup; -import eu.dnetlib.dhp.schema.oaf.Datasource; -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.*; import eu.dnetlib.dhp.schema.oaf.utils.OafMapperUtils; @ExtendWith(MockitoExtension.class) @@ -63,22 +61,32 @@ public class MigrateDbEntitiesApplicationTest { } @Test - public void testProcessDatasource() throws Exception { - final List fields = prepareMocks("datasources_resultset_entry.json"); + public void testProcessService() throws Exception { + final List fields = prepareMocks("services_resultset_entry.json"); - final List list = app.processDatasource(rs); + final List list = app.processService(rs); assertEquals(1, list.size()); verifyMocks(fields); final Datasource ds = (Datasource) list.get(0); 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("englishname", fields), ds.getEnglishname().getValue()); - assertEquals(getValueAsString("contactemail", fields), ds.getContactemail().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("collectedfromname", fields), ds.getCollectedfrom().get(0).getValue()); assertEquals(getValueAsString("officialname", fields), ds.getJournal().getName()); assertEquals(getValueAsString("issnPrinted", fields), ds.getJournal().getIssnPrinted()); assertEquals(getValueAsString("issnOnline", fields), ds.getJournal().getIssnOnline()); @@ -90,19 +98,98 @@ public class MigrateDbEntitiesApplicationTest { assertEquals("pubsrepository::journal", ds.getDatasourcetypeui().getClassid()); 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(null, ds.getDataprovider()); + assertEquals(null, ds.getServiceprovider()); + + 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("eosc:jurisdictions", ds.getJurisdiction().getSchemeid()); assertTrue(ds.getThematic()); - assertTrue(ds.getKnowledgegraph()); - assertEquals(1, ds.getContentpolicies().size()); - assertEquals("Journal article", ds.getContentpolicies().get(0).getClassid()); - assertEquals("eosc:contentpolicies", ds.getContentpolicies().get(0).getSchemeid()); + HashSet cpSchemeId = ds + .getContentpolicies() + .stream() + .map(Qualifier::getSchemeid) + .collect(Collectors.toCollection(HashSet::new)); + assertTrue(cpSchemeId.size() == 1); + assertTrue(cpSchemeId.contains("eosc:contentpolicies")); + HashSet 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.getFulltextdownload()); assertEquals("2022-03-11", ds.getConsenttermsofusedate()); + assertEquals("2022-03-11", ds.getLastconsenttermsofusedate()); } @Test @@ -154,7 +241,7 @@ public class MigrateDbEntitiesApplicationTest { public void testProcessDatasourceOrganization() throws Exception { final List fields = prepareMocks("datasourceorganization_resultset_entry.json"); - final List list = app.processDatasourceOrganization(rs); + final List list = app.processServiceOrganization(rs); assertEquals(2, list.size()); verifyMocks(fields); @@ -356,18 +443,31 @@ public class MigrateDbEntitiesApplicationTest { } private Float getValueAsFloat(final String name, final List 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 fields) { + final Object value = getValueAs(name, fields); + return value != null ? new Double(value.toString()) : null; + } + + private Integer getValueAsInt(final String name, final List fields) { + final Object value = getValueAs(name, fields); + return value != null ? new Integer(value.toString()) : null; } private T getValueAs(final String name, final List fields) { - return fields + final Optional field = fields .stream() .filter(f -> f.getField().equals(name)) - .map(TypedField::getValue) - .filter(Objects::nonNull) - .map(o -> (T) o) .findFirst() - .get(); + .map(TypedField::getValue) + .map(o -> (T) o); + if (!field.isPresent()) { + return null; + } + return field.get(); } private List getValueAsList(final String name, final List fields) { diff --git a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala b/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala deleted file mode 100644 index b90827e81..000000000 --- a/dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/sx/pangaea/PangaeaTransformTest.scala +++ /dev/null @@ -1,29 +0,0 @@ -package eu.dnetlib.dhp.sx.pangaea - -import eu.dnetlib.dhp.sx.graph.pangaea.PangaeaUtils -import org.junit.jupiter.api.Test - -import java.util.TimeZone -import java.text.SimpleDateFormat -import java.util.Date -import scala.io.Source -class PangaeaTransformTest { - - - - @Test - def test_dateStamp() :Unit ={ - - - - val d = new Date() - - val s:String = s"${new SimpleDateFormat("yyyy-MM-dd'T'HH:mm:ss.SSS")format d}Z" - println(s) - - - val xml = Source.fromInputStream(getClass.getResourceAsStream("input.xml")).mkString - println(PangaeaUtils.parseXml(xml)) - } - -} diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json new file mode 100644 index 000000000..b7c51d810 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/publication_clean_context.json @@ -0,0 +1,7 @@ +{"author":[],"bestaccessright":{"classid":"OPEN","classname":"Open Access","schemeid":"dnet:access_modes","schemename":"dnet:access_modes"},"collectedfrom":[{"dataInfo":null,"key":"10|openaire____::c6df70599aa984f16ee52b4b86d2e89f","value":"DANS (Data Archiving and Networked 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Geography)"}],"versioning":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":true},"websiteurl":{"dataInfo":{"deletedbyinference":false,"inferred":false,"invisible":false,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"Harvested","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"},"trust":"0.900"},"value":"http://www.snsb.info/dwb_biocase.html"}} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json index 6f2b7aa7d..64627dd2b 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_cris.json @@ -1 +1,5 @@ -{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire-cris_1.1" }} \ No newline at end of file +{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire-cris_1.1" }, + "originalId": ["eurocrisdris::1234"], + "collectedfrom": [{"key": "eurocrisdris::2b29d08e383ff4cd8a2b6b226ce37e38", "value": "Directory of Research Information System (DRIS)"}], + "pid": [{"value": "10.1010.xyx", "qualifier": {"classid": "doi"}}] +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json index e2db47943..cb2916a27 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/merge/datasource_openaire2.0.json @@ -1 +1,4 @@ -{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire2.0" }} \ No newline at end of file +{ "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", "openairecompatibility": { "classid": "openaire2.0" }, + "originalId": ["opendoar____::1234"], + "collectedfrom": [{"key": "openaire____::47ce9e9f4fad46e732cff06419ecaabb", "value": "OpenDOAR"}] +} \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json index 06b0d483b..a41fac8b8 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasourceorganization_resultset_entry.json @@ -1,6 +1,6 @@ [ { - "field": "datasource", + "field": "service", "type": "string", "value": "openaire____::revistasunicauca" }, diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml index f4b0c477f..277578185 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/oaf_record.xml @@ -60,6 +60,15 @@ https://oneecosystem.pensoft.net/article/13718/ One Ecosystem 0001 + ror_________::https://ror.org/02gdcn153 + corda_______::226852 diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo.xml new file mode 100644 index 000000000..0fc568e56 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/odf_zenodo.xml @@ -0,0 +1,69 @@ + +> +

+ oai:zenodo.org:3406824 + 2020-01-20T16:45:20Z + openaire + 2022-06-07T10:21:24.06Z + test________::92fe3efa47883b2f3401e6a4bd92e9d7 + 2020-05-21T05:26:15.93Z + 2020-08-01T11:06:26.977Z +
+ + + 10.5281/zenodo.3406824 + + http://dx.doi.org/10.5281/zenodo.3406824 + + + + Anne van Weerden + 0000-0003-3272-8007 + Utrecht University Library + + + Anne van, Weerden + 0000-0003-3272-8008 + Utrecht University Library + + + + Helen Bayly and Catherine Disney as influences in the life of Sir William Rowan Hamilton + + Zenodo + 2018 + + Sir William Rowan Hamilton, Lady Helena Maria Hamilton Bayly, Catherine Disney, Ireland, history, biography, nineteenth century + + + 2018-12-28 + + en + + + 10.5281/zenodo.3406823 + + + Creative Commons Attribution 4.0 International + Open Access + + +

In the 1880s Robert Graves published a biography about Sir William Rowan Hamilton (1805-1865), to which in a 1980 biography Thomas Hankins added further information. From these biographies a picture emerged of a man who was unhappily married because he had lost the love of his life, which raised the question how such an unhappy man could produce so much beautiful mathematics. In this article it is stated that a main cause for the unhappy picture is that Graves ignored the influence on one another of Hamilton and his wife Helen Bayly, and Hankins that of Hamilton and his first and lost love Catherine Disney. It is then shown that if these influences are taken into account a very different view on Hamilton;s private life arises, in which he was happily married to a wife who enabled him to work as he needed to.

 + + + 10.5281/zenodo.3406824 + 0001 + 2018-12-28 + OPEN + https://creativecommons.org/licenses/by/4.0/legalcode + eng + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml new file mode 100644 index 000000000..ca3ebe6c2 --- /dev/null +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/rohub.xml @@ -0,0 +1,103 @@ + + +
+ eosca5322f5f::4dd1aaf93ae136b65dc9ee4e6f76eac9 + 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + 2022-05-25T15:35:48.262Z + eosca5322f5f + 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + 2022-05-25T15:35:38Z + rohub_data + ro-crate_data + 2022-05-25T15:36:11.094Z +
+ + + https://w3id.org/ro-id/53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + + http://api.rohub.org/api/ros/53aa90bf-c593-4e6d-923f-d4711ac4b0e1/ + + + + https://github.com/NordicESMhub/RELIANCE/blob/main/content/science/notebooks/air_quality_lockdown.ipynb + + https://github.com/NordicESMhub/RELIANCE/blob/main/content/science/notebooks/air_quality_lockdown.ipynb + + https://nordicesmhub.github.io/RELIANCE/science/notebooks/air_quality_lockdown.html + + https://nordicesmhub.github.io/RELIANCE/science/notebooks/air_quality_lockdown.html + + + + + Anne Fouilloux + + + + + 2021-12-19T21:18:33Z + + + The COVID-19 pandemic has led to significant reductions in economic activity, especially during lockdowns. Several studies has shown that the concentration of nitrogen dioxyde and particulate matter levels have reduced during lockdown events. Reductions in transportation sector emissions are most likely largely responsible for the NO2 anomalies. In this study, we analyze the impact of lockdown events on the air quality using data from Copernicus Atmosphere Monitoring Service over Europe and at selected locations. + + + + European Commission + 10.13039/501100000781 + 101017502 + Research Lifecycle Management for Earth Science Communities and Copernicus Users + + + MIT License + University of Oslo + 2021 + RO-crate + + open access + + + 11.971 MB + + + Applied sciences + Meteorology + EOSC::RO-crate + + + Impact of the Covid-19 Lockdown on Air quality over Europe + + + https://w3id.org/ro-id/53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + 0048 + + OPEN + https://opensource.org/licenses/MIT + und + + + + + + + https%3A%2F%2Fapi.rohub.org%2Fapi%2Foai2d%2F + 53aa90bf-c593-4e6d-923f-d4711ac4b0e1 + 2022-05-25T15:35:38Z + + + + + false + false + 0.9 + + + + + \ No newline at end of file diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json similarity index 69% rename from dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json rename to dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json index 11b884cde..3614c5266 100644 --- a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/datasources_resultset_entry.json +++ b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/raw/services_resultset_entry.json @@ -1,18 +1,51 @@ [ { - "field": "datasourceid", + "field": "id", "type": "string", "value": "274269ac6f3b::2579-5449" }, { - "field": "identities", + "field": "originalid", "type": "array", "value": [ - "274269ac6f3b::2579-5449", + "fairsharing_::1562", "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", "type": "string", @@ -23,16 +56,6 @@ "type": "string", "value": "Jurnal Ilmiah Pendidikan Scholastic" }, - { - "field": "contactemail", - "type": "string", - "value": "test@test.it" - }, - { - "field": "openairecompatibility", - "type": "string", - "value": "hostedBy@@@dnet:datasourceCompatibilityLevel" - }, { "field": "websiteurl", "type": "string", @@ -44,11 +67,14 @@ "value": null }, { - "field": "accessinfopackage", - "type": "array", - "value": [ - null - ] + "field": "contactemail", + "type": "string", + "value": "test@test.it" + }, + { + "field": "namespaceprefix", + "type": "string", + "value": "ojs_25795449" }, { "field": "latitude", @@ -61,9 +87,19 @@ "value": 0 }, { - "field": "namespaceprefix", + "field": "dateofvalidation", + "type": "date", + "value": null + }, + { + "field": "description", "type": "string", - "value": "ojs_25795449" + "value": "veterinary medicine" + }, + { + "field": "subjects", + "type": "array", + "value": [] }, { "field": "odnumberofitems", @@ -75,16 +111,6 @@ "type": "date", "value": null }, - { - "field": "subjects", - "type": "array", - "value": null - }, - { - "field": "description", - "type": "string", - "value": null - }, { "field": "odpolicies", "type": "string", @@ -93,44 +119,33 @@ { "field": "odlanguages", "type": "array", - "value": [] - }, - { - "field": "odcontenttypes", - "type": "array", "value": [ - "Journal articles" + "English", + "German", + "French", + "Danish", + "Norwegian", + "Swedish" ] }, { - "field": "inferred", - "type": "boolean", - "value": false + "field": "languages", + "type": "array", + "value": [ + "English", + "German", + "French", + "Danish", + "Norwegian", + "Swedish" + ] }, { - "field": "deletedbyinference", - "type": "boolean", - "value": false - }, - { - "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": "accessinfopackage", + "type": "array", + "value": [ + "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai" + ] }, { "field": "releasestartdate", @@ -147,16 +162,6 @@ "type": "string", "value": null }, - { - "field": "dataprovider", - "type": "boolean", - "value": null - }, - { - "field": "serviceprovider", - "type": "boolean", - "value": null - }, { "field": "databaseaccesstype", "type": "string", @@ -183,12 +188,12 @@ "value": null }, { - "field": "citationguidelineurl", - "type": "string", + "field": "versioncontrol", + "type": "boolean", "value": null }, { - "field": "qualitymanagementkind", + "field": "citationguidelineurl", "type": "string", "value": null }, @@ -208,29 +213,38 @@ "value": [] }, { - "field": "collectedfromid", - "type": "string", - "value": "openaire____::SnVybmFsIEZha3VsdGFzIFNhc3RyYSBVbml2ZXJzaXRhcyBFa2FzYWt0aQ==" + "field": "inferred", + "type": "boolean", + "value": false }, { - "field": "collectedfromname", - "type": "string", - "value": "Jurnal Fakultas Sastra Universitas Ekasakti" + "field": "deletedbyinference", + "type": "boolean", + "value": false }, { - "field": "datasourcetype", - "type": "string", - "value": "pubsrepository::journal@@@dnet:datasource_typologies" + "field": "trust", + "type": "double", + "value": 0.9 }, { - "field": "datasourcetypeui", + "field": "inferenceprovenance", "type": "string", - "value": "pubsrepository::journal@@@dnet:datasource_typologies_ui" + "value": null }, { - "field": "provenanceaction", - "type": "not_used", - "value": "sysimport:crosswalk:entityregistry@@@dnet:provenance_actions" + "field": "dateofcollection", + "type": "date", + "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", @@ -247,6 +261,13 @@ "type": "string", "value": "2579-5447" }, + { + "field": "researchentitytypes", + "type": "array", + "value": [ + "Research Data" + ] + }, { "field": "jurisdiction", "type": "string", @@ -257,16 +278,36 @@ "type": "boolean", "value": true }, - { - "field": "knowledgegraph", - "type": "boolean", - "value": true - }, { "field": "contentpolicies", "type": "array", "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 +324,10 @@ "field": "consenttermsofusedate", "type": "date", "value": "2022-03-11" + }, + { + "field": "lastconsenttermsofusedate", + "type": "date", + "value": "2022-03-11" } ] diff --git a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/datasource/datasource_10.json.gz b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/datasource/datasource_10.json.gz index 130dd4c36..10a4ec591 100644 Binary files a/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/datasource/datasource_10.json.gz and b/dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/sample/datasource/datasource_10.json.gz differ 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 5d4a831c0..b34ec9693 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 @@ -535,6 +535,12 @@ public class XmlRecordFactory implements Serializable { if (ds.getDatasourcetypeui() != null) { 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) { metadata .add( @@ -583,6 +589,16 @@ public class XmlRecordFactory implements Serializable { metadata .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) { metadata .add( @@ -609,6 +625,16 @@ public class XmlRecordFactory implements Serializable { .map(c -> XmlSerializationUtils.asXmlElement("odlanguages", c.getValue())) .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) { metadata .addAll( @@ -689,18 +715,18 @@ public class XmlRecordFactory implements Serializable { XmlSerializationUtils .asXmlElement("versioning", ds.getVersioning().getValue().toString())); } + if (ds.getVersioncontrol() != null) { + metadata + .add( + XmlSerializationUtils + .asXmlElement("versioncontrol", ds.getVersioncontrol().toString())); + } if (ds.getCitationguidelineurl() != null) { metadata .add( XmlSerializationUtils .asXmlElement("citationguidelineurl", ds.getCitationguidelineurl().getValue())); } - if (ds.getQualitymanagementkind() != null) { - metadata - .add( - XmlSerializationUtils - .asXmlElement("qualitymanagementkind", ds.getQualitymanagementkind().getValue())); - } if (ds.getPidsystems() != null) { metadata .add(XmlSerializationUtils.asXmlElement("pidsystems", ds.getPidsystems().getValue())); @@ -722,17 +748,24 @@ public class XmlRecordFactory implements Serializable { if (ds.getJournal() != null) { metadata.add(XmlSerializationUtils.mapJournal(ds.getJournal())); } - if (ds.getSubjects() != null) { + if (ds.getResearchentitytypes() != null) { metadata .addAll( ds - .getSubjects() + .getResearchentitytypes() .stream() - .filter(Objects::nonNull) - .map(sp -> XmlSerializationUtils.mapStructuredProperty("subjects", sp)) + .map(c -> XmlSerializationUtils.asXmlElement("researchentitytypes", c)) + .collect(Collectors.toList())); + } + if (ds.getProvidedproducttypes() != null) { + metadata + .addAll( + ds + .getProvidedproducttypes() + .stream() + .map(c -> XmlSerializationUtils.asXmlElement("providedproducttypes", c)) .collect(Collectors.toList())); } - if (ds.getJurisdiction() != null) { metadata.add(XmlSerializationUtils.mapQualifier("jurisdiction", ds.getJurisdiction())); } @@ -741,11 +774,6 @@ public class XmlRecordFactory implements Serializable { metadata.add(XmlSerializationUtils.asXmlElement("thematic", ds.getThematic().toString())); } - if (ds.getKnowledgegraph() != null) { - metadata - .add(XmlSerializationUtils.asXmlElement("knowledgegraph", ds.getKnowledgegraph().toString())); - } - if (ds.getContentpolicies() != null) { metadata .addAll( @@ -756,7 +784,34 @@ public class XmlRecordFactory implements Serializable { .map(q -> XmlSerializationUtils.mapQualifier("contentpolicy", q)) .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; case organization: final Organization o = (Organization) entity; @@ -944,17 +999,11 @@ public class XmlRecordFactory implements Serializable { private List measuresAsXml(List measures) { return measures .stream() - .flatMap( - m -> m - .getUnit() - .stream() - .map( - u -> Lists - .newArrayList( - new Tuple2<>("id", m.getId()), - new Tuple2<>("key", u.getKey()), - new Tuple2<>("value", u.getValue()))) - .map(l -> XmlSerializationUtils.asXmlElement("measure", l))) + .map(m -> { + List> l = Lists.newArrayList(new Tuple2<>("id", m.getId())); + m.getUnit().forEach(kv -> l.add(new Tuple2<>(kv.getKey(), kv.getValue()))); + return XmlSerializationUtils.asXmlElement("measure", l); + }) .collect(Collectors.toList()); } diff --git a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/sx/provision/scholix_index.json b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/sx/provision/scholix_index.json index 93032712a..86e80206f 100644 --- a/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/sx/provision/scholix_index.json +++ b/dhp-workflows/dhp-graph-provision/src/main/resources/eu/dnetlib/dhp/sx/provision/scholix_index.json @@ -41,7 +41,8 @@ } }, "publicationDate": { - "type": "keyword" + "type": "date", + "format": "yyyy-MM-dd" }, "relationship": { "properties": { diff --git a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java index c32d868e8..92d9f497f 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java +++ b/dhp-workflows/dhp-graph-provision/src/test/java/eu/dnetlib/dhp/oa/provision/XmlRecordFactoryTest.java @@ -11,6 +11,7 @@ import java.util.List; import org.apache.commons.io.IOUtils; import org.dom4j.Document; import org.dom4j.DocumentException; +import org.dom4j.Element; import org.dom4j.io.SAXReader; import org.junit.jupiter.api.Test; @@ -72,11 +73,20 @@ public class XmlRecordFactoryTest { assertEquals("EUR", doc.valueOf("//processingchargecurrency/text()")); assertEquals( - "1.00889953098e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@value")); + "5.06690394631e-09", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@score")); assertEquals( - "30.6576853333", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@value")); + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'influence']/@class")); + assertEquals( - "4.62970429725e-08", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@value")); + "0.0", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@score")); + assertEquals( + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity_alt']/@class")); + + assertEquals( + "3.11855618382e-09", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@score")); + assertEquals( + "C", doc.valueOf("//*[local-name() = 'result']/measure[./@id = 'popularity']/@class")); + } @Test @@ -142,7 +152,7 @@ public class XmlRecordFactoryTest { } @Test - public void testDatasource() throws IOException, DocumentException { + public void testService() throws IOException, DocumentException { final ContextMapper contextMapper = new ContextMapper(); final XmlRecordFactory xmlRecordFactory = new XmlRecordFactory(contextMapper, false, @@ -167,6 +177,14 @@ public class XmlRecordFactoryTest { assertEquals("true", doc.valueOf("//thematic")); assertEquals("Journal article", doc.valueOf("//contentpolicy/@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()); } } diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json index ae069b8b5..ce6b10826 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/datasource.json @@ -1 +1,388 @@ -{"collectedfrom":[{"key":"10|openaire____::13068d7823ea0bd86516ac2cb66e96ba","value":"Jurnal Fakultas Sastra Universitas Ekasakti","dataInfo":null}],"dataInfo":{"invisible":false,"inferred":false,"deletedbyinference":false,"trust":"0.900","inferenceprovenance":null,"provenanceaction":{"classid":"sysimport:crosswalk:entityregistry","classname":"sysimport:crosswalk:entityregistry","schemeid":"dnet:provenanceActions","schemename":"dnet:provenanceActions"}},"lastupdatetimestamp":1645012035118,"id":"10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7","originalId":["274269ac6f3b::2579-5449","piwik:13"],"pid":[],"dateofcollection":"2020-01-21","dateoftransformation":null,"extraInfo":[],"oaiprovenance":null,"datasourcetype":{"classid":"pubsrepository::journal","classname":"pubsrepository::journal","schemeid":"dnet:datasource_typologies","schemename":"dnet:datasource_typologies"},"datasourcetypeui":{"classid":"pubsrepository::journal","classname":"Journal 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Fakultas Sastra Universitas Ekasakti", + "dataInfo": null + } + ], + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + }, + "lastupdatetimestamp": 1645012035118, + "id": "10|274269ac6f3b::2a2e2793b500f3f7b47ef24b1a9277b7", + "originalId": [ + "274269ac6f3b::2579-5449", + "piwik:13" + ], + "dateofcollection": "2020-01-21", + "dateoftransformation": null, + "extraInfo": [], + "oaiprovenance": null, + "datasourcetype": { + "classid": "pubsrepository::journal", + "classname": "Journal", + "schemeid": "dnet:datasource_typologies", + "schemename": "dnet:datasource_typologies" + }, + "datasourcetypeui": { + "classid": "pubsrepository::journal", + "classname": "Journal archive", + "schemeid": "dnet:datasource_typologies_ui", + "schemename": "dnet:datasource_typologies_ui" + }, + "pid": [ + { + "value": "r3d100010218", + "qualifier": { + "classid": "re3data", + "classname": "Registry of research data repositories", + "schemeid": "dnet:pid_types", + "schemename": "dnet:pid_types" + } + } + ], + "eosctype": { + "classid": "Data Source", + "classname": "Data Source", + "schemeid": "dnet:eosc_types", + "schemename": "dnet:eosc_types" + }, + "eoscdatasourcetype": { + "classid": "Journal archive", + "classname": "Journal archive", + "schemeid": "dnet:eosc_datasource_types", + "schemename": "dnet:eosc_datasource_types" + }, + "openairecompatibility": { + "classid": "hostedBy", + "classname": "hostedBy", + "schemeid": "dnet:datasourceCompatibilityLevel", + "schemename": "dnet:datasourceCompatibilityLevel" + }, + "officialname": { + "value": "Jurnal Ilmiah Pendidikan Scholastic", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "englishname": { + "value": "Jurnal Ilmiah Pendidikan Scholastic", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "websiteurl": { + "value": "http://e-journal.sastra-unes.com/index.php/JIPS/index", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "logourl": null, + "contactemail": { + "value": "test@test.it", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "namespaceprefix": { + "value": "ojs_25795449", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "latitude": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "longitude": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "dateofvalidation": null, + "description": { + "value": "veterinary medicine", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "subjects": [], + "odnumberofitems": { + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "odnumberofitemsdate": null, + "odpolicies": null, + "odlanguages": [ + { + "value": "English", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "value": "German", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "languages" : [ "English", "German" ], + "accessinfopackage": [ + { + "value": "http://www.revista.vocesdelaeducacion.com.mx/index.php/index/oai", + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ], + "releasestartdate": null, + "releaseenddate": null, + "missionstatementurl": null, + "dataprovider": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "serviceprovider": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "databaseaccesstype": null, + "datauploadtype": null, + "databaseaccessrestriction": null, + "datauploadrestriction": null, + "versioning": { + "value": false, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "versioncontrol": false, + "citationguidelineurl": null, + "qualitymanagementkind": null, + "pidsystems": null, + "certificates": null, + "policies": [], + "journal": { + "name": "Jurnal Ilmiah Pendidikan Scholastic", + "issnPrinted": "2579-5449", + "issnOnline": "2579-5448", + "issnLinking": "2579-5447", + "ep": null, + "iss": null, + "sp": null, + "vol": null, + "edition": null, + "conferenceplace": null, + "conferencedate": null, + "dataInfo": { + "invisible": false, + "inferred": false, + "deletedbyinference": false, + "trust": "0.900", + "inferenceprovenance": null, + "provenanceaction": { + "classid": "sysimport:crosswalk:entityregistry", + "classname": "sysimport:crosswalk:entityregistry", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + "researchentitytypes":[ "Research Data" ], + "providedentitytypes": null, + "providedproducttypes": null, + "jurisdiction": { + "classid": "National", + "classname": "National", + "schemeid": "eosc:jurisdictions", + "schemename": "eosc:jurisdictions" + }, + "thematic": true, + "contentpolicies": [ + { + "classid": "Journal article", + "classname": "Journal article", + "schemeid": "eosc:contentpolicies", + "schemename": "eosc:contentpolicies" + } + ], + "submissionpolicyurl": null, + "preservationpolicyurl" : "Permanent Archiving https://datadryad.org/stash/faq", + "researchproductaccesspolicies": [ + "https://100percentit.com/legal/" + ], + "researchproductmetadataaccesspolicies": [ + "https://wenmr.science.uu.nl/conditions" + ] +} diff --git a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json index 2c52ce269..41ced45ae 100644 --- a/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json +++ b/dhp-workflows/dhp-graph-provision/src/test/resources/eu/dnetlib/dhp/oa/provision/publication.json @@ -5,7 +5,37 @@ "unit": [ { "key": "score", - "value": "1.00889953098e-08" + "value": "5.06690394631e-09", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] }, @@ -14,7 +44,37 @@ "unit": [ { "key": "score", - "value": "30.6576853333" + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] }, @@ -23,7 +83,115 @@ "unit": [ { "key": "score", - "value": "4.62970429725e-08" + "value": "3.11855618382e-09", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ] + }, + { + "id": "influence_alt", + "unit": [ + { + "key": "score", + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + } + ] + }, + { + "id": "impulse", + "unit": [ + { + "key": "score", + "value": "0.0", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } + }, + { + "key": "class", + "value": "C", + "dataInfo": { + "invisible": false, + "inferred": true, + "deletedbyinference": false, + "trust": "", + "inferenceprovenance": "update", + "provenanceaction": { + "classid": "measure:bip", + "classname": "Inferred by OpenAIRE", + "schemeid": "dnet:provenanceActions", + "schemename": "dnet:provenanceActions" + } + } } ] } diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql index a5839da11..aee66fd5e 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step13.sql @@ -80,4 +80,34 @@ where reltype='resultResult' and r2.datainfo.deletedbyinference=false and r2.datainfo.invisible = FALSE and r1.resulttype.classname != 'other' and r2.resulttype.classname != 'other' - and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; \ No newline at end of file + and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE; + +create table ${stats_db_name}.result_citations_oc stored as parquet as +select substr(target, 4) as id, count(distinct substr(source, 4)) as citations +from ${openaire_db_name}.relation rel +join ${openaire_db_name}.result r1 on rel.source=r1.id +join ${openaire_db_name}.result r2 on r2.id=rel.target +where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:crosswalk:opencitations' + and reltype='resultResult' + and r1.resulttype.classname!=r2.resulttype.classname + and r1.datainfo.deletedbyinference=false and r1.datainfo.invisible = FALSE + and r2.datainfo.deletedbyinference=false and r2.datainfo.invisible = FALSE + and r1.resulttype.classname != 'other' + and r2.resulttype.classname != 'other' + and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE +group by substr(target, 4); + +create table ${stats_db_name}.result_references_oc stored as parquet as +select substr(source, 4) as id, count(distinct substr(target, 4)) as references +from ${openaire_db_name}.relation rel + join ${openaire_db_name}.result r1 on rel.source=r1.id + join ${openaire_db_name}.result r2 on r2.id=rel.target +where relClass='Cites' and rel.datainfo.provenanceaction.classid = 'sysimport:crosswalk:opencitations' + and reltype='resultResult' + and r1.resulttype.classname!=r2.resulttype.classname + and r1.datainfo.deletedbyinference=false and r1.datainfo.invisible = FALSE + and r2.datainfo.deletedbyinference=false and r2.datainfo.invisible = FALSE + and r1.resulttype.classname != 'other' + and r2.resulttype.classname != 'other' + and rel.datainfo.deletedbyinference=false and rel.datainfo.invisible = FALSE +group by substr(source, 4); \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql index a95ee74d8..db40cf973 100755 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step16-createIndicatorsTables.sql @@ -12,6 +12,8 @@ and (ri.accessright = 'Open Access' or ri.accessright = 'Embargo' or ri.accessright = 'Open Source')) tmp on p.id= tmp.id; +compute stats indi_pub_green_oa; + create table indi_pub_grey_lit stored as parquet as select distinct p.id, coalesce(grey_lit, 0) as grey_lit from publication p @@ -22,6 +24,8 @@ join result_classifications rt on rt.id = p.id where rt.type not in ('Article','Part of book or chapter of book','Book','Doctoral thesis','Master thesis','Data Paper', 'Thesis', 'Bachelor thesis', 'Conference object') and not exists (select 1 from result_classifications rc where type ='Other literature type' and rc.id=p.id)) tmp on p.id=tmp.id; +compute stats indi_pub_grey_lit; + create table indi_pub_doi_from_crossref stored as parquet as select distinct p.id, coalesce(doi_from_crossref, 0) as doi_from_crossref from publication p @@ -31,6 +35,7 @@ join datasource d on d.id = ri.collectedfrom where pidtype='Digital Object Identifier' and d.name ='Crossref') tmp on tmp.id=p.id; +compute stats indi_pub_doi_from_crossref; ---- Sprint 2 ---- create table indi_result_has_cc_licence stored as parquet as select distinct r.id, (case when lic='' or lic is null then 0 else 1 end) as has_cc_license @@ -40,6 +45,8 @@ join result_licenses as license on license.id = r.id where lower(license.type) LIKE '%creativecommons.org%' OR lower(license.type) LIKE '%cc-%') tmp on r.id= tmp.id; +compute stats indi_result_has_cc_licence; + create table indi_result_has_cc_licence_url stored as parquet as select distinct r.id, case when lic_host='' or lic_host is null then 0 else 1 end as has_cc_license_url from result r @@ -49,16 +56,21 @@ join result_licenses as license on license.id = r.id WHERE lower(parse_url(license.type, "HOST")) = "creativecommons.org") tmp on r.id= tmp.id; +compute stats indi_result_has_cc_licence_url; + create table indi_pub_has_abstract stored as parquet as select distinct publication.id, coalesce(abstract, 1) has_abstract from publication; +compute stats indi_pub_has_abstract; + create table indi_result_with_orcid stored as parquet as select distinct r.id, coalesce(has_orcid, 0) as has_orcid from result r left outer join (select id, 1 as has_orcid from result_orcid) tmp on r.id= tmp.id; +compute stats indi_result_with_orcid; ---- Sprint 3 ---- create table indi_funded_result_with_fundref stored as parquet as @@ -68,27 +80,33 @@ left outer join (select distinct id, 1 as fundref from project_results where provenance='Harvested') tmp on r.id= tmp.id; -create table indi_result_org_country_collab stored as parquet as -with tmp as -(select o.id as id, o.country , ro.id as result,r.type from organization o -join result_organization ro on o.id=ro.organization -join result r on r.id=ro.id where o.country <> 'UNKNOWN') -select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 -join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id and o1.country<>o2.country -group by o1.id, o1.type,o2.country; +compute stats indi_funded_result_with_fundref; -create table indi_result_org_collab stored as parquet as -with tmp as -(select o.id, ro.id as result,r.type from organization o -join result_organization ro on o.id=ro.organization -join result r on r.id=ro.id) -select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations -from tmp as o1 -join tmp as o2 on o1.result=o2.result -where o1.id<>o2.id -group by o1.id, o2.id, o1.type; +-- create table indi_result_org_country_collab stored as parquet as +-- with tmp as +-- (select o.id as id, o.country , ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id where o.country <> 'UNKNOWN') +-- select o1.id org1,o2.country country2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id and o1.country<>o2.country +-- group by o1.id, o1.type,o2.country; +-- +-- compute stats indi_result_org_country_collab; + +-- create table indi_result_org_collab stored as parquet as +-- with tmp as +-- (select o.id, ro.id as result,r.type from organization o +-- join result_organization ro on o.id=ro.organization +-- join result r on r.id=ro.id) +-- select o1.id org1,o2.id org2, o1.type, count(distinct o1.result) as collaborations +-- from tmp as o1 +-- join tmp as o2 on o1.result=o2.result +-- where o1.id<>o2.id +-- group by o1.id, o2.id, o1.type; +-- +-- compute stats indi_result_org_collab; create table indi_funder_country_collab stored as parquet as with tmp as (select funder, project, country from organization_projects op @@ -101,6 +119,8 @@ join tmp as f2 on f1.project=f2.project where f1.country<>f2.country group by f1.funder, f2.country, f1.country; +compute stats indi_funder_country_collab; + create table indi_result_country_collab stored as parquet as with tmp as (select country, ro.id as result,r.type from organization o @@ -112,6 +132,8 @@ join tmp as o2 on o1.result=o2.result where o1.country<>o2.country group by o1.country, o2.country, o1.type; +compute stats indi_result_country_collab; + ---- Sprint 4 ---- create table indi_pub_diamond stored as parquet as select distinct pd.id, coalesce(in_diamond_journal, 0) as in_diamond_journal @@ -123,6 +145,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=true or ps.journal_is_oa=true) and ps.has_apc=false) tmp on pd.id=tmp.id; +compute stats indi_pub_diamond; + create table indi_pub_hybrid stored as parquet as select distinct pd.id, coalesce(is_hybrid, 0) as is_hybrid from publication_datasources pd @@ -133,6 +157,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and (ps.journal_is_in_doaj=false and ps.journal_is_oa=false)) tmp on pd.id=tmp.id; +compute stats indi_pub_hybrid; + create table indi_pub_in_transformative stored as parquet as select distinct pd.id, coalesce(is_transformative, 0) as is_transformative from publication pd @@ -143,6 +169,8 @@ join stats_ext.plan_s_jn ps where (ps.issn_print=d.issn_printed and ps.issn_onli and ps.is_transformative_journal=true) tmp on pd.id=tmp.id; +compute stats indi_pub_in_transformative; + create table indi_pub_closed_other_open stored as parquet as select distinct ri.id, coalesce(pub_closed_other_open, 0) as pub_closed_other_open from result_instance ri left outer join @@ -153,11 +181,12 @@ where d.type like '%Journal%' and ri.accessright='Closed Access' and (p.bestlicence='Open Access' or p.bestlicence='Open Source')) tmp on tmp.id=ri.id; - +compute stats indi_pub_closed_other_open; ---- Sprint 5 ---- create table indi_result_no_of_copies stored as parquet as select id, count(id) as number_of_copies from result_instance group by id; +compute stats indi_result_no_of_copies; ---- Sprint 6 ---- create table indi_pub_gold_oa stored as parquet as WITH gold_oa AS ( @@ -183,6 +212,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_pub_gold_oa; + create table indi_datasets_gold_oa stored as parquet as WITH gold_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn @@ -210,6 +241,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_datasets_gold_oa; + create table indi_software_gold_oa stored as parquet as WITH gold_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_1 as issn @@ -237,6 +270,8 @@ LEFT OUTER JOIN ( JOIN issn on issn.id=pd.datasource JOIN gold_oa on issn.issn = gold_oa.issn) tmp ON pd.id=tmp.id; +compute stats indi_software_gold_oa; + create table indi_org_findable stored as parquet as with result_with_pid as ( select ro.organization organization, count(distinct rp.id) no_result_with_pid from result_organization ro @@ -263,6 +298,8 @@ join result_with_pid_share on result_with_pid_share.organization=allresults.orga left outer join ( select organization, abstract_share from result_with_abstract_share) tmp on tmp.organization=allresults.organization; +compute stats indi_org_findable; + create table indi_org_openess stored as parquet as WITH datasets_oa as ( SELECT ro.organization, count(dg.id) no_oadatasets FROM indi_datasets_gold_oa dg @@ -313,6 +350,8 @@ left outer join ( left outer join ( select organization,s from allsoftwaresshare) tmp1 on tmp1.organization=allpubsshare.organization; +compute stats indi_org_openess; + create table indi_pub_hybrid_oa_with_cc stored as parquet as WITH hybrid_oa AS ( SELECT issn_l, journal_is_in_doaj, journal_is_oa, issn_print as issn @@ -343,6 +382,8 @@ LEFT OUTER JOIN ( JOIN indi_result_has_cc_licence cc on pd.id=cc.id where cc.has_cc_license=1) tmp on pd.id=tmp.id; +compute stats indi_pub_hybrid_oa_with_cc; + create table indi_pub_downloads stored as parquet as SELECT result_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -350,6 +391,8 @@ where downloads>0 GROUP BY result_id order by no_dowloads desc; +compute stats indi_pub_downloads; + create table indi_pub_downloads_datasource stored as parquet as SELECT result_id, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats join publication on result_id=id @@ -357,15 +400,21 @@ where downloads>0 GROUP BY result_id, repository_id order by result_id; +compute stats indi_pub_downloads_datasource; + create table indi_pub_downloads_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, `year` order by `year` asc; +compute stats indi_pub_downloads_year; + create table indi_pub_downloads_datasource_year stored as parquet as SELECT result_id, substring(us.`date`, 1,4) as `year`, repository_id, sum(downloads) no_dowloads from openaire_prod_usage_stats.usage_stats us join publication on result_id=id where downloads>0 GROUP BY result_id, repository_id, `year` order by `year` asc, result_id; + +compute stats indi_pub_downloads_datasource_year; \ No newline at end of file diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql index bcc9f0b5d..7412910a9 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step20-createMonitorDB.sql @@ -18,28 +18,45 @@ create table TARGET.result stored as parquet as select * from SOURCE.result r where exists (select 1 from SOURCE.result_concepts rc where rc.id=r.id) union all select * from SOURCE.result r where exists (select 1 from SOURCE.result_organization ro where ro.id=r.id and ro.organization in ( - 'openorgs____::759d59f05d77188faee99b7493b46805', - 'openorgs____::b84450f9864182c67b8611b5593f4250', - 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', - 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', - 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', - 'openorgs____::d169c7407dd417152596908d48c11460', - 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', - 'openorgs____::2fb1e47b4612688d9de9169d579939a7', - 'openorgs____::759d59f05d77188faee99b7493b46805', - 'openorgs____::cad284878801b9465fa51a95b1d779db', - 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', - 'openorgs____::c0286313e36479eff8676dba9b724b40' - -- ,'openorgs____::c80a8243a5e5c620d7931c88d93bf17a' -- Paris Diderot - ) )) foo; + 'openorgs____::b84450f9864182c67b8611b5593f4250', --"Athena Research and Innovation Center In Information Communication & Knowledge Technologies', --ARC" + 'openorgs____::d41cf6bd4ab1b1362a44397e0b95c975', --National Research Council + 'openorgs____::d2a09b9d5eabb10c95f9470e172d05d2', --??? Not exists ?? + 'openorgs____::d169c7407dd417152596908d48c11460', --Masaryk University + 'openorgs____::1ec924b1759bb16d0a02f2dad8689b21', --University of Belgrade + 'openorgs____::2fb1e47b4612688d9de9169d579939a7', --University of Helsinki + 'openorgs____::759d59f05d77188faee99b7493b46805', --University of Minho + 'openorgs____::cad284878801b9465fa51a95b1d779db', --Universidad Politécnica de Madrid + 'openorgs____::eadc8da90a546e98c03f896661a2e4d4', --University of Göttingen + 'openorgs____::c0286313e36479eff8676dba9b724b40', --National and Kapodistrian University of Athens + -- 'openorgs____::c80a8243a5e5c620d7931c88d93bf17a', --Université Paris Diderot + 'openorgs____::c08634f0a6b0081c3dc6e6c93a4314f3', --Bielefeld University + 'openorgs____::6fc85e4a8f7ecaf4b0c738d010e967ea', --University of Southern Denmark + 'openorgs____::3d6122f87f9a97a99d8f6e3d73313720', --Humboldt-Universität zu Berlin + 'openorgs____::16720ada63d0fa8ca41601feae7d1aa5', --TU Darmstadt + 'openorgs____::ccc0a066b56d2cfaf90c2ae369df16f5', --KU Leuven + 'openorgs____::4c6f119632adf789746f0a057ed73e90', --University of the Western Cape + 'openorgs____::ec3665affa01aeafa28b7852c4176dbd', --Rudjer Boskovic Institute + 'openorgs____::5f31346d444a7f06a28c880fb170b0f6', --Ghent University + 'openorgs____::2dbe47117fd5409f9c61620813456632', --University of Luxembourg + 'openorgs____::6445d7758d3a40c4d997953b6632a368' --National Institute of Informatics (NII) + ) )) foo; compute stats TARGET.result; create table TARGET.result_citations stored as parquet as select * from SOURCE.result_citations orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_citations; +create table TARGET.result_references_oc stored as parquet as select * from SOURCE.result_references_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_references_oc; + +create table TARGET.result_citations_oc stored as parquet as select * from SOURCE.result_citations_oc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_citations_oc; + create table TARGET.result_classifications stored as parquet as select * from SOURCE.result_classifications orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_classifications; +create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); +compute stats TARGET.result_apc; + create table TARGET.result_concepts stored as parquet as select * from SOURCE.result_concepts orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_concepts; @@ -90,11 +107,6 @@ compute stats TARGET.result_sources; create table TARGET.result_topics stored as parquet as select * from SOURCE.result_topics orig where exists (select 1 from TARGET.result r where r.id=orig.id); compute stats TARGET.result_topics; -create table TARGET.result_apc stored as parquet as select * from SOURCE.result_apc orig where exists (select 1 from TARGET.result r where r.id=orig.id); -compute stats TARGET.result_apc; - - - create view TARGET.foo1 as select * from SOURCE.result_result rr where rr.source in (select id from TARGET.result); create view TARGET.foo2 as select * from SOURCE.result_result rr where rr.target in (select id from TARGET.result); create table TARGET.result_result STORED AS PARQUET as select distinct * from (select * from TARGET.foo1 union all select * from TARGET.foo2) foufou; diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql index e1c36cbc0..b5eba6111 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step7.sql @@ -127,6 +127,7 @@ CREATE TABLE ${stats_db_name}.result_organization STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r WHERE r.reltype = 'resultOrganization' + and r.target like '50|%' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.result_projects STORED AS PARQUET AS diff --git a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql index fa3eca1a9..6fa0e6fdf 100644 --- a/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql +++ b/dhp-workflows/dhp-stats-update/src/main/resources/eu/dnetlib/dhp/oa/graph/stats/oozie_app/scripts/step8.sql @@ -93,7 +93,7 @@ where d.datainfo.deletedbyinference=false and d.datainfo.invisible=false; CREATE TABLE ${stats_db_name}.datasource_organizations STORED AS PARQUET AS SELECT substr(r.target, 4) AS id, substr(r.source, 4) AS organization FROM ${openaire_db_name}.relation r -WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.datainfo.invisible=false; +WHERE r.reltype = 'datasourceOrganization' and r.datainfo.deletedbyinference = false and r.target like '20|%' and r.datainfo.invisible=false; -- datasource sources: -- where the datasource info have been collected from. diff --git a/pom.xml b/pom.xml index 136b9b867..54070f654 100644 --- a/pom.xml +++ b/pom.xml @@ -801,7 +801,7 @@ 3.3.3 3.4.2 [2.12,3.0) - [2.10.32] + [2.12.0] [4.0.3] [6.0.5] [3.1.6]