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Merge branch 'master' of https://code-repo.d4science.org/D-Net/dnet-hadoop

This commit is contained in:
Miriam Baglioni 2023-08-09 13:07:13 +02:00
parent 9e8e39f78a 0bc74e2000
commit 599828ce35
18 changed files with 298 additions and 28 deletions
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10
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/FundRefCleaningRule.java
View File

@ -6,14 +6,16 @@ import java.util.regex.Pattern;
public class FundRefCleaningRule {
public static String clean(final String fundrefId) {
public static final Pattern PATTERN = Pattern.compile("\\d+");
String s = fundrefId
public static String clean(final String fundRefId) {
String s = fundRefId
.toLowerCase()
.replaceAll("\\s", "");
Matcher m = Pattern.compile("\\d+").matcher(s);
if (m.matches()) {
Matcher m = PATTERN.matcher(s);
if (m.find()) {
return m.group();
} else {
return "";

70
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GraphCleaningFunctions.java
View File

@ -13,11 +13,7 @@ import java.util.stream.Collectors;
import java.util.stream.Stream;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.api.java.function.MapFunction;
import org.apache.spark.sql.Encoders;
import com.fasterxml.jackson.core.JsonProcessingException;
import com.fasterxml.jackson.databind.ObjectMapper;
import com.github.sisyphsu.dateparser.DateParserUtils;
import com.google.common.collect.Lists;
import com.google.common.collect.Sets;
@ -39,6 +35,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
public static final String TITLE_FILTER_REGEX = String.format("(%s)|\\W|\\d", TITLE_TEST);
public static final int TITLE_FILTER_RESIDUAL_LENGTH = 5;
private static final String NAME_CLEANING_REGEX = "[\\r\\n\\t\\s]+";
public static <T extends Oaf> T cleanContext(T value, String contextId, String verifyParam) {
if (ModelSupport.isSubClass(value, Result.class)) {
@ -228,7 +225,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
}
public static <T extends Oaf> boolean filter(T value) {
if (Boolean.TRUE
if (!(value instanceof Relation) && (Boolean.TRUE
.equals(
Optional
.ofNullable(value)
@ -239,15 +236,16 @@ public class GraphCleaningFunctions extends CleaningFunctions {
d -> Optional
.ofNullable(d.getInvisible())
.orElse(true))
.orElse(true))
.orElse(true))) {
.orElse(false))
.orElse(true)))) {
return true;
}
if (value instanceof Datasource) {
// nothing to evaluate here
} else if (value instanceof Project) {
// nothing to evaluate here
final Project p = (Project) value;
return Objects.nonNull(p.getCode()) && StringUtils.isNotBlank(p.getCode().getValue());
} else if (value instanceof Organization) {
// nothing to evaluate here
} else if (value instanceof Relation) {
@ -294,6 +292,13 @@ public class GraphCleaningFunctions extends CleaningFunctions {
} else if (value instanceof Result) {
Result r = (Result) value;
if (Objects.nonNull(r.getFulltext())
&& (ModelConstants.SOFTWARE_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()) ||
ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
r.setFulltext(null);
}
if (Objects.nonNull(r.getDateofacceptance())) {
Optional<String> date = cleanDateField(r.getDateofacceptance());
if (date.isPresent()) {
@ -318,8 +323,18 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(sp -> StringUtils.isNotBlank(sp.getValue()))
.collect(Collectors.toList()));
}
if (Objects.nonNull(r.getPublisher()) && StringUtils.isBlank(r.getPublisher().getValue())) {
r.setPublisher(null);
if (Objects.nonNull(r.getPublisher())) {
if (StringUtils.isBlank(r.getPublisher().getValue())) {
r.setPublisher(null);
} else {
r
.getPublisher()
.setValue(
r
.getPublisher()
.getValue()
.replaceAll(NAME_CLEANING_REGEX, " "));
}
}
if (Objects.isNull(r.getLanguage()) || StringUtils.isBlank(r.getLanguage().getClassid())) {
r
@ -486,6 +501,11 @@ public class GraphCleaningFunctions extends CleaningFunctions {
i.setDateofacceptance(null);
}
}
if (StringUtils.isNotBlank(i.getFulltext()) &&
(ModelConstants.SOFTWARE_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()) ||
ModelConstants.DATASET_RESULTTYPE_CLASSID.equals(r.getResulttype().getClassid()))) {
i.setFulltext(null);
}
}
}
if (Objects.isNull(r.getBestaccessright())
@ -510,6 +530,7 @@ public class GraphCleaningFunctions extends CleaningFunctions {
.filter(Objects::nonNull)
.filter(a -> StringUtils.isNotBlank(a.getFullname()))
.filter(a -> StringUtils.isNotBlank(a.getFullname().replaceAll("[\\W]", "")))
.map(GraphCleaningFunctions::cleanupAuthor)
.collect(Collectors.toList()));
boolean nullRank = r
@ -604,6 +625,35 @@ public class GraphCleaningFunctions extends CleaningFunctions {
return value;
}
private static Author cleanupAuthor(Author author) {
if (StringUtils.isNotBlank(author.getFullname())) {
author
.setFullname(
author
.getFullname()
.replaceAll(NAME_CLEANING_REGEX, " ")
.replace("\"", "\\\""));
}
if (StringUtils.isNotBlank(author.getName())) {
author
.setName(
author
.getName()
.replaceAll(NAME_CLEANING_REGEX, " ")
.replace("\"", "\\\""));
}
if (StringUtils.isNotBlank(author.getSurname())) {
author
.setSurname(
author
.getSurname()
.replaceAll(NAME_CLEANING_REGEX, " ")
.replace("\"", "\\\""));
}
return author;
}
private static Optional<String> cleanDateField(Field<String> dateofacceptance) {
return Optional
.ofNullable(dateofacceptance)

10
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/GridCleaningRule.java
View File

@ -6,13 +6,19 @@ import java.util.regex.Pattern;
public class GridCleaningRule {
public static final Pattern PATTERN = Pattern.compile("(?<grid>\\d{4,6}\\.[0-9a-z]{1,2})");
public static String clean(String grid) {
String s = grid
.replaceAll("\\s", "")
.toLowerCase();
Matcher m = Pattern.compile("\\d{4,6}\\.[0-9a-z]{1,2}").matcher(s);
return m.matches() ? "grid." + m.group() : "";
Matcher m = PATTERN.matcher(s);
if (m.find()) {
return "grid." + m.group("grid");
}
return "";
}
}

6
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/ISNICleaningRule.java
View File

@ -7,10 +7,12 @@ import java.util.regex.Pattern;
// https://www.wikidata.org/wiki/Property:P213
public class ISNICleaningRule {
public static final Pattern PATTERN = Pattern.compile("([0]{4}) ?([0-9]{4}) ?([0-9]{4}) ?([0-9]{3}[0-9X])");
public static String clean(final String isni) {
Matcher m = Pattern.compile("([0]{4}) ?([0-9]{4}) ?([0-9]{4}) ?([0-9]{3}[0-9X])").matcher(isni);
if (m.matches()) {
Matcher m = PATTERN.matcher(isni);
if (m.find()) {
return String.join("", m.group(1), m.group(2), m.group(3), m.group(4));
} else {
return "";

6
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PICCleaningRule.java
View File

@ -6,10 +6,12 @@ import java.util.regex.Pattern;
public class PICCleaningRule {
public static final Pattern PATTERN = Pattern.compile("\\d{9}");
public static String clean(final String pic) {
Matcher m = Pattern.compile("\\d{9}").matcher(pic);
if (m.matches()) {
Matcher m = PATTERN.matcher(pic);
if (m.find()) {
return m.group();
} else {
return "";

13
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PmcCleaningRule.java
View File

@ -1,13 +1,24 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class PmcCleaningRule {
public static final Pattern PATTERN = Pattern.compile("PMC\\d{1,8}");
public static String clean(String pmc) {
String s = pmc
.replaceAll("\\s", "")
.toUpperCase();
return s.matches("^PMC\\d{1,8}$") ? s : "";
final Matcher m = PATTERN.matcher(s);
if (m.find()) {
return m.group();
}
return "";
}
}

17
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/PmidCleaningRule.java
View File

@ -1,16 +1,25 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
// https://researchguides.stevens.edu/c.php?g=442331&p=6577176
public class PmidCleaningRule {
public static final Pattern PATTERN = Pattern.compile("[1-9]{1,8}");
public static String clean(String pmid) {
String s = pmid
.toLowerCase()
.replaceAll("\\s", "")
.trim()
.replaceAll("^0+", "");
return s.matches("^\\d{1,8}$") ? s : "";
.replaceAll("\\s", "");
final Matcher m = PATTERN.matcher(s);
if (m.find()) {
return m.group();
}
return "";
}
}

13
dhp-common/src/main/java/eu/dnetlib/dhp/schema/oaf/utils/RorCleaningRule.java
View File

@ -7,12 +7,21 @@ import java.util.regex.Pattern;
// https://ror.readme.io/docs/ror-identifier-pattern
public class RorCleaningRule {
public static final String ROR_PREFIX = "https://ror.org/";
private static final Pattern PATTERN = Pattern.compile("(?<ror>0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2})");
public static String clean(String ror) {
String s = ror
.replaceAll("\\s", "")
.toLowerCase();
Matcher m = Pattern.compile("0[a-hj-km-np-tv-z|0-9]{6}[0-9]{2}").matcher(s);
return m.matches() ? "https://ror.org/" + m.group() : "";
Matcher m = PATTERN.matcher(s);
if (m.find()) {
return ROR_PREFIX + m.group("ror");
}
return "";
}
}

18
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/GridCleaningRuleTest.java Normal file
View File

@ -0,0 +1,18 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class GridCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("grid.493784.5", GridCleaningRule.clean("grid.493784.5"));
assertEquals("grid.493784.5x", GridCleaningRule.clean("grid.493784.5x"));
assertEquals("grid.493784.5x", GridCleaningRule.clean("493784.5x"));
assertEquals("", GridCleaningRule.clean("493x784.5x"));
}
}

19
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/ISNICleaningRuleTest.java Normal file
View File

@ -0,0 +1,19 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class ISNICleaningRuleTest {
@Test
void testCleaning() {
assertEquals("0000000463436020", ISNICleaningRule.clean("0000 0004 6343 6020"));
assertEquals("0000000463436020", ISNICleaningRule.clean("0000000463436020"));
assertEquals("", ISNICleaningRule.clean("Q30256598"));
assertEquals("0000000493403529", ISNICleaningRule.clean("ISNI:0000000493403529"));
assertEquals("000000008614884X", ISNICleaningRule.clean("0000 0000 8614 884X"));
}
}

19
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PICCleaningRuleTest.java Normal file
View File

@ -0,0 +1,19 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class PICCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("887624982", PICCleaningRule.clean("887624982"));
assertEquals("", PICCleaningRule.clean("887 624982"));
assertEquals("887624982", PICCleaningRule.clean(" 887624982 "));
assertEquals("887624982", PICCleaningRule.clean(" 887624982x "));
assertEquals("887624982", PICCleaningRule.clean(" 88762498200 "));
}
}

19
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PmcCleaningRuleTest.java Normal file
View File

@ -0,0 +1,19 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class PmcCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("PMC1234", PmcCleaningRule.clean("PMC1234"));
assertEquals("PMC1234", PmcCleaningRule.clean(" PMC1234"));
assertEquals("PMC12345678", PmcCleaningRule.clean("PMC12345678"));
assertEquals("PMC12345678", PmcCleaningRule.clean("PMC123456789"));
assertEquals("PMC12345678", PmcCleaningRule.clean("PMC 12345678"));
}
}

18
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/PmidCleaningRuleTest.java Normal file
View File

@ -0,0 +1,18 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class PmidCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("1234", PmidCleaningRule.clean("01234"));
assertEquals("1234567", PmidCleaningRule.clean("0123 4567"));
assertEquals("123", PmidCleaningRule.clean("0123x4567"));
assertEquals("", PmidCleaningRule.clean("abc"));
}
}

17
dhp-common/src/test/java/eu/dnetlib/dhp/schema/oaf/utils/RorCleaningRuleTest.java Normal file
View File

@ -0,0 +1,17 @@
package eu.dnetlib.dhp.schema.oaf.utils;
import static org.junit.jupiter.api.Assertions.assertEquals;
import org.junit.jupiter.api.Test;
class RorCleaningRuleTest {
@Test
void testCleaning() {
assertEquals("https://ror.org/05rpz9w55", RorCleaningRule.clean("https://ror.org/05rpz9w55"));
assertEquals("https://ror.org/05rpz9w55", RorCleaningRule.clean("05rpz9w55"));
assertEquals("", RorCleaningRule.clean("05rpz9w_55"));
}
}

40
dhp-workflows/dhp-graph-mapper/src/test/java/eu/dnetlib/dhp/oa/graph/clean/GraphCleaningFunctionsTest.java
View File

@ -251,6 +251,12 @@ public class GraphCleaningFunctionsTest {
pid.getQualifier().getClassname()));
});
assertTrue(
p_cleaned
.getAuthor()
.stream()
.anyMatch(a -> "Brien, Tom".equals(a.getFullname())));
assertNotNull(p_cleaned.getSubject());
List<Subject> fos_subjects = p_cleaned
@ -285,6 +291,31 @@ public class GraphCleaningFunctionsTest {
System.out.println(MAPPER.writeValueAsString(p_cleaned));
}
@Test
void testCleaning_dataset() throws Exception {
assertNotNull(vocabularies);
assertNotNull(mapping);
String json = IOUtils
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/result_dataset.json"));
Dataset p_in = MAPPER.readValue(json, Dataset.class);
assertTrue(p_in instanceof Result);
assertTrue(p_in instanceof Dataset);
Dataset p_out = OafCleaner.apply(GraphCleaningFunctions.fixVocabularyNames(p_in), mapping);
assertNotNull(p_out);
assertNotNull(p_out.getPublisher());
assertNotNull(p_out.getPublisher().getValue());
Dataset p_cleaned = GraphCleaningFunctions.cleanup(p_out, vocabularies);
assertEquals("Best publisher in the world", p_cleaned.getPublisher().getValue());
}
private static void verify_keyword(Publication p_cleaned, String subject) {
Optional<Subject> s1 = p_cleaned
.getSubject()
@ -337,6 +368,15 @@ public class GraphCleaningFunctionsTest {
Assertions.assertEquals(true, GraphCleaningFunctions.filter(cleaned));
}
@Test
public void testFilterProject() throws IOException {
String json = IOUtils
.toString(getClass().getResourceAsStream("/eu/dnetlib/dhp/oa/graph/clean/project.json"));
Project p_in = MAPPER.readValue(json, Project.class);
Assertions.assertEquals(false, GraphCleaningFunctions.filter(p_in));
}
@Test
public void testCleanDoiBoost2() throws IOException {
String json = IOUtils

1
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/project.json Normal file
View File

@ -0,0 +1 @@
{"measures": [{"id": "downloads", "unit": [{"dataInfo": {"provenanceaction": {"classid": "measure:usage_counts", "classname": "measure:usage_counts", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "count", "value": "1"}]}, {"id": "views", "unit": [{"dataInfo": {"provenanceaction": {"classid": "measure:usage_counts", "classname": "measure:usage_counts", "schemeid": "dnet:provenanceActions", "schemename": "dnet:provenanceActions"}, "deletedbyinference": false, "inferred": true, "inferenceprovenance": "update", "invisible": false, "trust": ""}, "key": "count", "value": "0"}]}], "id": "40|aka_________::591da07706352f1195afaeed4065f52e"}

2
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result.json
View File

@ -3,7 +3,7 @@
{
"affiliation": [
],
"fullname": "Brien, Tom",
"fullname": "Brien, Tom",
"name": "Tom",
"pid": [
{

28
dhp-workflows/dhp-graph-mapper/src/test/resources/eu/dnetlib/dhp/oa/graph/clean/result_dataset.json Normal file
View File

@ -0,0 +1,28 @@
{
"resulttype": {
"classid": "dataset",
"classname": "dataset",
"schemeid": "dnet:result_typologies",
"schemename": "dnet:result_typologies"
},
"fulltext": [
{
"value" : "https://www.researchgate.net"
}
],
"publisher" : {
"value" : "Best publisher in the world"
},
"id": "50|CSC_________::2250a70c903c6ac6e4c01438259e9375",
"instance": [
{
"instancetype": {
"classid": "Comment/debate",
"classname": "Comment/debate",
"schemeid": "dnet:publication_resource",
"schemename": "dnet:publication_resource"
},
"fulltext": "https://www.researchgate.net"
}
]
}