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orcid-no-doi #43

Merged
claudio.atzori merged 45 commits from enrico.ottonello/dnet-hadoop:orcid-no-doi into master 2020-12-02 10:55:12 +01:00
Conversation 5 Commits 45 Files Changed 68 +128 -39
3 changed files with 128 additions and 39 deletions
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47
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/SparkGenEnrichedOrcidWorks.java
View File

@ -17,10 +17,12 @@ 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.util.LongAccumulator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.JsonElement;
import com.google.gson.JsonParser;
@ -93,17 +95,48 @@ public class SparkGenEnrichedOrcidWorks {
.toJavaRDD();
enrichedWorksRDD.saveAsTextFile(workingPath + outputEnrichedWorksPath);
logger.info("Works enriched data saved");
JavaRDD<Publication> oafPublicationRDD = enrichedWorksRDD.map(e -> {
JsonElement j = new JsonParser().parse(e._2());
return (Publication) PublicationToOaf
.generatePublicationActionsFromDump(j.getAsJsonObject());
}).filter(p -> p != null);
final LongAccumulator parsedPublications = spark.sparkContext().longAccumulator("parsedPublications");
final LongAccumulator enrichedPublications = spark
.sparkContext()
.longAccumulator("enrichedPublications");
final LongAccumulator errorsGeneric = spark.sparkContext().longAccumulator("errorsGeneric");
final LongAccumulator errorsInvalidTitle = spark.sparkContext().longAccumulator("errorsInvalidTitle");
final LongAccumulator errorsNotFoundAuthors = spark
.sparkContext()
.longAccumulator("errorsNotFoundAuthors");
final LongAccumulator errorsInvalidType = spark.sparkContext().longAccumulator("errorsInvalidType");
final PublicationToOaf publicationToOaf = new PublicationToOaf(
parsedPublications,
enrichedPublications,
errorsGeneric,
errorsInvalidTitle,
errorsNotFoundAuthors,
errorsInvalidType);
JavaRDD<Publication> oafPublicationRDD = enrichedWorksRDD
.map(
e -> {
return (Publication) publicationToOaf
.generatePublicationActionsFromJson(e._2());
})
.filter(p -> p != null);
Dataset<Publication> publicationDataset = spark
.createDataset(
oafPublicationRDD.repartition(1).rdd(),
oafPublicationRDD.rdd(),
Encoders.bean(Publication.class));
publicationDataset.write().mode(SaveMode.Overwrite).save(workingPath + "no_doi_dataset/output");
publicationDataset
.write()
.format("parquet")
.mode(SaveMode.Overwrite)
.save(workingPath + "no_doi_dataset/output");
logger.info("parsedPublications: " + parsedPublications.value().toString());
logger.info("enrichedPublications: " + enrichedPublications.value().toString());
logger.info("errorsGeneric: " + errorsGeneric.value().toString());
logger.info("errorsInvalidTitle: " + errorsInvalidTitle.value().toString());
logger.info("errorsNotFoundAuthors: " + errorsNotFoundAuthors.value().toString());
logger.info("errorsInvalidType: " + errorsInvalidType.value().toString());
});
}

117
dhp-workflows/dhp-doiboost/src/main/java/eu/dnetlib/doiboost/orcidnodoi/oaf/PublicationToOaf.java
View File

@ -3,18 +3,17 @@ package eu.dnetlib.doiboost.orcidnodoi.oaf;
import static eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility.*;
import java.io.Serializable;
import java.util.*;
import java.util.stream.Collectors;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.spark.util.LongAccumulator;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.gson.Gson;
import com.google.gson.JsonArray;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.*;
import eu.dnetlib.dhp.common.PacePerson;
import eu.dnetlib.dhp.schema.oaf.*;
@ -22,7 +21,7 @@ import eu.dnetlib.dhp.utils.DHPUtils;
import eu.dnetlib.doiboost.orcidnodoi.util.DumpToActionsUtility;
import eu.dnetlib.doiboost.orcidnodoi.util.Pair;
public class PublicationToOaf {
public class PublicationToOaf implements Serializable {
static Logger logger = LoggerFactory.getLogger(PublicationToOaf.class);
@ -31,6 +30,37 @@ public class PublicationToOaf {
public static final String OPENAIRE_PREFIX = "openaire____";
public static final String SEPARATOR = "::";
private final LongAccumulator parsedPublications;
private final LongAccumulator enrichedPublications;
private final LongAccumulator errorsGeneric;
private final LongAccumulator errorsInvalidTitle;
private final LongAccumulator errorsNotFoundAuthors;
private final LongAccumulator errorsInvalidType;
public PublicationToOaf(
LongAccumulator parsedPublications,
LongAccumulator enrichedPublications,
LongAccumulator errorsGeneric,
LongAccumulator errorsInvalidTitle,
LongAccumulator errorsNotFoundAuthors,
LongAccumulator errorsInvalidType) {
this.parsedPublications = parsedPublications;
this.enrichedPublications = enrichedPublications;
this.errorsGeneric = errorsGeneric;
this.errorsInvalidTitle = errorsInvalidTitle;
this.errorsNotFoundAuthors = errorsNotFoundAuthors;
this.errorsInvalidType = errorsInvalidType;
}
public PublicationToOaf() {
this.parsedPublications = null;
this.enrichedPublications = null;
this.errorsGeneric = null;
this.errorsInvalidTitle = null;
this.errorsNotFoundAuthors = null;
this.errorsInvalidType = null;
}
private static Map<String, Pair<String, String>> datasources = new HashMap<String, Pair<String, String>>() {
{
@ -69,11 +99,27 @@ public class PublicationToOaf {
public static final String PID_TYPES = "dnet:pid_types";
public static Oaf generatePublicationActionsFromDump(final JsonObject rootElement) {
public Oaf generatePublicationActionsFromJson(final String json) {
try {
if (parsedPublications != null) {
parsedPublications.add(1);
}
JsonElement jElement = new JsonParser().parse(json);
JsonObject jObject = jElement.getAsJsonObject();
return generatePublicationActionsFromDump(jObject);
} catch (Throwable t) {
logger.error("creating publication: " + t.getMessage());
if (errorsGeneric != null) {
errorsGeneric.add(1);
}
return null;
}
}
public Oaf generatePublicationActionsFromDump(final JsonObject rootElement) {
claudio.atzori commented 2020-09-21 16:08:46 +02:00
Review
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Is the caller expecting the null? Otherwise this would likely produce a NPE.

Is the caller expecting the `null`? Otherwise this would likely produce a NPE.
enrico.ottonello commented 2020-10-22 14:40:36 +02:00
Review
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yes, there is a filter for null value:
JavaRDD oafPublicationRDD = enrichedWorksRDD
.map(
e -> {
return (Publication) publicationToOaf
.generatePublicationActionsFromJson(e._2());
})
.filter(p -> p != null);

yes, there is a filter for null value: JavaRDD<Publication> oafPublicationRDD = enrichedWorksRDD .map( e -> { return (Publication) publicationToOaf .generatePublicationActionsFromJson(e._2()); }) .filter(p -> p != null);
logger.debug("generatePublicationActionsFromDump ...");
if (!isValid(rootElement/* , context */)) {
logger.error("publication not valid");
if (!isValid(rootElement)) {
return null;
}
@ -122,8 +168,9 @@ public class PublicationToOaf {
// Adding titles
final List<String> titles = createRepeatedField(rootElement, "titles");
if (titles == null || titles.isEmpty()) {
logger.error("titles not found");
// context.incrementCounter("filtered", "title_not_found", 1);
if (errorsInvalidTitle != null) {
errorsInvalidTitle.add(1);
}
return null;
}
Qualifier q = mapQualifier("main title", "main title", "dnet:dataCite_title", "dnet:dataCite_title");
@ -189,8 +236,9 @@ public class PublicationToOaf {
publication.setInstance(Arrays.asList(instance));
} else {
logger.error("type not found");
// context.incrementCounter("filtered", "type_not_found", 1);
if (errorsInvalidType != null) {
errorsInvalidType.add(1);
}
return null;
}
@ -199,17 +247,21 @@ public class PublicationToOaf {
if (authors != null && authors.size() > 0) {
publication.setAuthor(authors);
claudio.atzori commented 2020-09-21 16:10:00 +02:00
Review
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Is the caller expecting the null? Otherwise this would likely produce a NPE.

Is the caller expecting the `null`? Otherwise this would likely produce a NPE.
enrico.ottonello commented 2020-10-22 14:46:24 +02:00
Review
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yes, there is a filter on null value:
JavaRDD oafPublicationRDD = enrichedWorksRDD .map( e -> { return (Publication) publicationToOaf .generatePublicationActionsFromJson(e._2()); }) .filter(p -> p != null);

yes, there is a filter on null value: JavaRDD oafPublicationRDD = enrichedWorksRDD .map( e -> { return (Publication) publicationToOaf .generatePublicationActionsFromJson(e._2()); }) .filter(p -> p != null);
} else {
logger.error("authors not found");
// context.incrementCounter("filtered", "author_not_found", 1);
if (errorsNotFoundAuthors != null) {
errorsNotFoundAuthors.add(1);
}
return null;
}
String classValue = getDefaultResulttype(cobjValue);
publication
.setResulttype(mapQualifier(classValue, classValue, "dnet:result_typologies", "dnet:result_typologies"));
if (enrichedPublications != null) {
enrichedPublications.add(1);
claudio.atzori commented 2020-09-21 16:10:19 +02:00
Review
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Is the caller expecting the null? Otherwise this would likely produce a NPE.

Is the caller expecting the `null`? Otherwise this would likely produce a NPE.
enrico.ottonello commented 2020-10-22 14:47:09 +02:00
Review
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yes, there is a filter on null value: JavaRDD oafPublicationRDD = enrichedWorksRDD .map( e -> { return (Publication) publicationToOaf .generatePublicationActionsFromJson(e._2()); }) .filter(p -> p != null);

yes, there is a filter on null value: JavaRDD oafPublicationRDD = enrichedWorksRDD .map( e -> { return (Publication) publicationToOaf .generatePublicationActionsFromJson(e._2()); }) .filter(p -> p != null);
}
return publication;
}
public static List<Author> createAuthors(final JsonObject root) {
public List<Author> createAuthors(final JsonObject root) {
final String authorsJSONFieldName = "contributors";
@ -273,7 +325,7 @@ public class PublicationToOaf {
return null;
}
private static List<String> createRepeatedField(final JsonObject rootElement, final String fieldName) {
private List<String> createRepeatedField(final JsonObject rootElement, final String fieldName) {
if (!rootElement.has(fieldName)) {
return null;
}
claudio.atzori commented 2020-09-21 16:10:32 +02:00
Review
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Is the caller expecting the null? Otherwise this would likely produce a NPE.

Is the caller expecting the `null`? Otherwise this would likely produce a NPE.
enrico.ottonello commented 2020-10-22 14:48:26 +02:00
Review
Copy Link

yes, there is a check on null value

yes, there is a check on null value
@ -291,14 +343,14 @@ public class PublicationToOaf {
}
claudio.atzori commented 2020-09-21 16:11:13 +02:00
Review
Copy Link

Is the caller expecting the null? Otherwise this would likely produce a NPE.

Is the caller expecting the `null`? Otherwise this would likely produce a NPE.
enrico.ottonello commented 2020-10-22 14:50:41 +02:00
Review
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yes, there is a check on null value

yes, there is a check on null value
}
private static String cleanField(String value) {
private String cleanField(String value) {
if (value != null && !value.isEmpty() && value.charAt(0) == '"' && value.charAt(value.length() - 1) == '"') {
value = value.substring(1, value.length() - 1);
}
return value;
}
private static void settingRelevantDate(final JsonObject rootElement,
private void settingRelevantDate(final JsonObject rootElement,
final Publication publication,
final String jsonKey,
final String dictionaryKey,
@ -322,7 +374,7 @@ public class PublicationToOaf {
}
}
private static String getPublicationDate(final JsonObject rootElement,
private String getPublicationDate(final JsonObject rootElement,
final String jsonKey) {
JsonObject pubDateJson = null;
@ -358,24 +410,27 @@ public class PublicationToOaf {
return null;
}
protected static boolean isValid(final JsonObject rootElement/* , final Reporter context */) {
protected boolean isValid(final JsonObject rootElement/* , final Reporter context */) {
final String type = getStringValue(rootElement, "type");
if (!typologiesMapping.containsKey(type)) {
claudio.atzori commented 2020-09-21 16:12:15 +02:00
Review
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Is the caller expecting the null? Otherwise this would likely produce a NPE.

Is the caller expecting the `null`? Otherwise this would likely produce a NPE.
enrico.ottonello commented 2020-10-22 15:02:26 +02:00
Review
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yes, there is this ckeck on the value: StringUtils.isNotBlank

yes, there is this ckeck on the value: StringUtils.isNotBlank
logger.error("unknowntype_" + type);
// context.incrementCounter("filtered", "unknowntype_" + type, 1);
if (errorsInvalidType != null) {
errorsInvalidType.add(1);
}
return false;
}
if (!isValidJsonArray(rootElement, "titles")) {
logger.error("invalid_title");
// context.incrementCounter("filtered", "invalid_title", 1);
if (errorsInvalidTitle != null) {
errorsInvalidTitle.add(1);
}
return false;
}
return true;
}
private static boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) {
private boolean isValidJsonArray(final JsonObject rootElement, final String fieldName) {
if (!rootElement.has(fieldName)) {
return false;
}
@ -395,7 +450,7 @@ public class PublicationToOaf {
return true;
}
private static Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) {
private Qualifier mapQualifier(String classId, String className, String schemeId, String schemeName) {
final Qualifier qualifier = new Qualifier();
qualifier.setClassid(classId);
qualifier.setClassname(className);
@ -404,7 +459,7 @@ public class PublicationToOaf {
return qualifier;
}
private static ExternalReference convertExtRef(String extId, String classId, String className, String schemeId,
private ExternalReference convertExtRef(String extId, String classId, String className, String schemeId,
String schemeName) {
ExternalReference ex = new ExternalReference();
ex.setRefidentifier(extId);
@ -412,7 +467,7 @@ public class PublicationToOaf {
return ex;
}
private static StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) {
private StructuredProperty mapStructuredProperty(String value, Qualifier qualifier, DataInfo dataInfo) {
if (value == null | StringUtils.isBlank(value)) {
return null;
}
@ -424,7 +479,7 @@ public class PublicationToOaf {
return structuredProperty;
}
private static Field<String> mapStringField(String value, DataInfo dataInfo) {
private Field<String> mapStringField(String value, DataInfo dataInfo) {
if (value == null || StringUtils.isBlank(value)) {
return null;
}
@ -435,21 +490,21 @@ public class PublicationToOaf {
return stringField;
claudio.atzori commented 2020-09-21 16:15:17 +02:00
Review
Copy Link

Is the caller expecting the null? Otherwise this would likely produce a NPE.

Is the caller expecting the null? Otherwise this would likely produce a NPE.
enrico.ottonello commented 2020-10-22 15:24:16 +02:00
Review
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the value returned from this function is used to populate 2 fields of publication:
publication.setSource(value)
publication.setDateofacceptance(value)

the value returned from this function is used to populate 2 fields of publication: publication.setSource(value) publication.setDateofacceptance(value)
}
private static KeyValue createCollectedFrom() {
private KeyValue createCollectedFrom() {
KeyValue cf = new KeyValue();
cf.setValue(ORCID);
cf.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "806360c771262b4d6770e7cdf04b5c5a");
return cf;
}
private static KeyValue createHostedBy() {
private KeyValue createHostedBy() {
KeyValue hb = new KeyValue();
hb.setValue("Unknown Repository");
hb.setKey("10|" + OPENAIRE_PREFIX + SEPARATOR + "55045bd2a65019fd8e6741a755395c8c");
return hb;
}
private static StructuredProperty mapAuthorId(String orcidId) {
private StructuredProperty mapAuthorId(String orcidId) {
final StructuredProperty sp = new StructuredProperty();
sp.setValue(orcidId);
final Qualifier q = new Qualifier();

3
dhp-workflows/dhp-doiboost/src/test/java/eu/dnetlib/doiboost/orcidnodoi/PublicationToOafTest.java
View File

@ -27,7 +27,8 @@ public class PublicationToOafTest {
PublicationToOafTest.class.getResourceAsStream("publication.json"));
JsonElement j = new JsonParser().parse(jsonPublication);
logger.info("json publication loaded: " + j.toString());
Publication oafPublication = (Publication) PublicationToOaf
PublicationToOaf publicationToOaf = new PublicationToOaf();
Publication oafPublication = (Publication) publicationToOaf
.generatePublicationActionsFromDump(j.getAsJsonObject());
assertNotNull(oafPublication.getId());
assertNotNull(oafPublication.getOriginalId());