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TRM-29836: Create an UniProtKB result column to show publication DOI ids #202

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Nov 3, 2023
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TRM-29836: Create an UniProtKB result column to show publication DOI ids #202

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TRM-29836: Create an UniProtKB result column to show publication DOI ids
LeonardoGonzales Oct 27, 2023
fd67fde
code format with spotless automatic
Oct 27, 2023
2ed8b8a
Code review
LeonardoGonzales Nov 3, 2023
e6f9c29
code format with spotless automatic
Nov 3, 2023
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18 changes: 12 additions & 6 deletions core-parser/src/main/java/org/uniprot/core/parser/tsv/uniprot/EntryReferenceMap.java
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Original file line number Diff line number Diff line change
Expand Up @@ -9,7 +9,9 @@
import org.uniprot.core.uniprotkb.UniProtKBReference;

public class EntryReferenceMap implements NamedValueMap {
static final List<String> FIELDS = Arrays.asList("lit_pubmed_id");
static final String LIT_PUBMED_ID = "lit_pubmed_id";
static final String LIT_DOI_ID = "lit_doi_id";
static final List<String> FIELDS = Arrays.asList(LIT_PUBMED_ID, LIT_DOI_ID);
private final List<UniProtKBReference> references;

public EntryReferenceMap(List<UniProtKBReference> references) {
Expand All @@ -26,16 +28,20 @@ public Map<String, String> attributeValues() {
return Collections.emptyMap();
}

String result =
Map<CitationDatabase, String> idMaps =
references.stream()
.map(UniProtKBReference::getCitation)
.filter(val -> val.getCitationCrossReferences() != null)
.flatMap(val -> val.getCitationCrossReferences().stream())
.filter(val -> val.getDatabase().equals(CitationDatabase.PUBMED))
.map(CrossReference::getId)
.collect(Collectors.joining("; "));
.collect(
Collectors.groupingBy(
CrossReference::getDatabase,
Collectors.mapping(
CrossReference::getId, Collectors.joining("; "))));

Map<String, String> map = new HashMap<>();
map.put(FIELDS.get(0), result);
map.put(LIT_PUBMED_ID, idMaps.getOrDefault(CitationDatabase.PUBMED, ""));
map.put(LIT_DOI_ID, idMaps.getOrDefault(CitationDatabase.DOI, ""));
return map;
}

Expand Down
117 changes: 117 additions & 0 deletions core-parser/src/test/java/org/uniprot/core/parser/tsv/uniprot/EntryReferenceMapTest.java
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Original file line number Diff line number Diff line change
@@ -0,0 +1,117 @@
package org.uniprot.core.parser.tsv.uniprot;

import static org.junit.jupiter.api.Assertions.*;
import static org.uniprot.core.parser.tsv.uniprot.EntryReferenceMap.*;

import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import java.util.Map;

import org.junit.jupiter.api.Test;
import org.uniprot.core.citation.Citation;
import org.uniprot.core.citation.CitationDatabase;
import org.uniprot.core.citation.impl.ElectronicArticleBuilder;
import org.uniprot.core.impl.CrossReferenceBuilder;
import org.uniprot.core.uniprotkb.UniProtKBReference;
import org.uniprot.core.uniprotkb.impl.UniProtKBReferenceBuilder;

class EntryReferenceMapTest {

private static final String FIELD_SEPARATOR = "; ";

@Test
void testFields() {
List<String> expected = Arrays.asList(LIT_PUBMED_ID, LIT_DOI_ID);
assertEquals(expected, FIELDS);
}

@Test
void testLitDoiId() {
String doiId = "doiId1";
List<UniProtKBReference> references = getUniProtKBReferences(CitationDatabase.DOI, doiId);
EntryReferenceMap mapper = new EntryReferenceMap(references);
Map<String, String> result = mapper.attributeValues();

verifyFieldValue(result, LIT_DOI_ID, doiId);
}

@Test
void testMultipleLitDoiId() {
String doiId = "doiId1";
String doiId2 = "doiId2";
List<UniProtKBReference> references =
getUniProtKBReferences(CitationDatabase.DOI, doiId, doiId2);
EntryReferenceMap mapper = new EntryReferenceMap(references);
Map<String, String> result = mapper.attributeValues();

verifyFieldValue(result, LIT_DOI_ID, doiId + FIELD_SEPARATOR + doiId2);
}

@Test
void testLitPubmedId() {
String pubmedId = "pubmedId1";
List<UniProtKBReference> references =
getUniProtKBReferences(CitationDatabase.PUBMED, pubmedId);
EntryReferenceMap mapper = new EntryReferenceMap(references);
Map<String, String> result = mapper.attributeValues();

verifyFieldValue(result, LIT_PUBMED_ID, pubmedId);
}

@Test
void testMultipleLitPubmedId() {
String pubmedId = "pubmedId1";
String pubmedId2 = "pubmedId2";
List<UniProtKBReference> references =
getUniProtKBReferences(CitationDatabase.PUBMED, pubmedId, pubmedId2);

EntryReferenceMap mapper = new EntryReferenceMap(references);
Map<String, String> result = mapper.attributeValues();

verifyFieldValue(result, LIT_PUBMED_ID, pubmedId + FIELD_SEPARATOR + pubmedId2);
}

@Test
void testMixedIds() {
String pubmedId = "pubmedId1";
String pubmedId2 = "pubmedId2";
String doiId = "doiId1";
String doiId2 = "doiId2";
List<UniProtKBReference> references =
getUniProtKBReferences(CitationDatabase.PUBMED, pubmedId, pubmedId2);
references.addAll(getUniProtKBReferences(CitationDatabase.DOI, doiId, doiId2));

EntryReferenceMap mapper = new EntryReferenceMap(references);
Map<String, String> result = mapper.attributeValues();

verifyFieldValue(result, LIT_PUBMED_ID, pubmedId + FIELD_SEPARATOR + pubmedId2);
verifyFieldValue(result, LIT_DOI_ID, doiId + FIELD_SEPARATOR + doiId2);
}

private List<UniProtKBReference> getUniProtKBReferences(
CitationDatabase database, String... ids) {
List<UniProtKBReference> result = new ArrayList<>();
for (String id : ids) {
Citation citation =
new ElectronicArticleBuilder()
.citationCrossReferencesAdd(
new CrossReferenceBuilder<CitationDatabase>()
.database(database)
.id(id)
.build())
.build();
UniProtKBReference reference =
new UniProtKBReferenceBuilder().citation(citation).build();
result.add(reference);
}
return result;
}

private void verifyFieldValue(
Map<String, String> result, String fieldName, String expectedValue) {
String resultValue = result.get(fieldName);
assertNotNull(resultValue);
assertEquals(expectedValue, resultValue);
}
}