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tsv changes #243

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merged 2 commits into from
Oct 28, 2024
Merged

tsv changes #243

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e37a1be
tsv changes
supun-ebi Oct 24, 2024
d030c11
address review comments
supun-ebi Oct 25, 2024
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11 changes: 10 additions & 1 deletion ...arser/src/main/java/org/uniprot/core/parser/tsv/uniparc/UniParcEntryLightValueMapper.java
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Original file line number Diff line number Diff line change
@@ -1,6 +1,7 @@
package org.uniprot.core.parser.tsv.uniparc;

import org.uniprot.core.parser.tsv.EntityValueMapper;
import org.uniprot.core.uniparc.CommonOrganism;
import org.uniprot.core.uniparc.UniParcEntryLight;
import org.uniprot.core.uniprotkb.taxonomy.Organism;

Expand All @@ -19,7 +20,8 @@ public class UniParcEntryLightValueMapper implements EntityValueMapper<UniParcEn
"proteome",
"accession",
"first_seen",
"last_seen");
"last_seen",
"common_taxons");
private static final String DELIMITER2 = "; ";

@Override
Expand Down Expand Up @@ -93,6 +95,13 @@ private Map<String, String> getSimpleAttributeValues(UniParcEntryLight entry, Li
.map(LocalDate::toString)
.orElse(""));
break;
case "common_taxons":
map.put(
UNIPARC_FIELDS.get(9),
Optional.of(entry.getCommonTaxons())
.map(ct -> ct.stream().map(CommonOrganism::getCommonTaxon).collect(Collectors.joining("; ")))
.orElse(""));
break;
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default:
// do nothing
}
Expand Down
5 changes: 4 additions & 1 deletion ...r/src/test/java/org/uniprot/core/parser/tsv/uniparc/UniParcEntryLightValueMapperTest.java
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Expand Up @@ -21,7 +21,7 @@ class UniParcEntryLightValueMapperTest {
@Test
void testGetDataOrganism() {
UniParcEntryLight entry = create();
List<String> fields = Arrays.asList("upi", "organism", "organism_id", "proteome");
List<String> fields = Arrays.asList("upi", "organism", "organism_id", "proteome", "common_taxons");

Map<String, String> result = new UniParcEntryLightValueMapper().mapEntity(entry, fields);

Expand All @@ -30,6 +30,7 @@ void testGetDataOrganism() {
verify("Homo sapiens; MOUSE", "organism", result);
verify("9606; 10090", "organism_id", result);
verify("UP000005640:C1; UP000002494:C2", "proteome", result);
verify("Bacteroides; Enterococcus", "common_taxons", result);
}

@Test
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Expand Down Expand Up @@ -95,6 +96,7 @@ private UniParcEntryLight create() {

LinkedHashSet<String> proteinNames = new LinkedHashSet<>(List.of("protein1", "protein2"));
LinkedHashSet<String> geneNames = new LinkedHashSet<>(List.of("gene1", "gene2"));
List<CommonOrganism> commonTaxons = List.of(new CommonOrganismBuilder().commonTaxon("Bacteroides").build(),new CommonOrganismBuilder().commonTaxon("Enterococcus").build());
LinkedHashSet<Proteome> proteomes = new LinkedHashSet<>(List.of(new ProteomeBuilder().id("UP000005640").component("C1").build(), new ProteomeBuilder().id("UP000002494").component("C2").build()));

return new UniParcEntryLightBuilder()
Expand All @@ -103,6 +105,7 @@ private UniParcEntryLight create() {
.organismsSet(organisms)
.proteomesSet(proteomes)
.geneNamesSet(geneNames)
.commonTaxonsSet(commonTaxons)
.proteinNamesSet(proteinNames)
.mostRecentCrossRefUpdated(LocalDate.of(2020, 10, 25))
.oldestCrossRefCreated(LocalDate.of(2017, 2, 12))
Expand Down
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