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Merge pull request #65 from ebi-uniprot/GOA-2316-separate-descendants…
…-slim-converters separate descendants and slimming filter converters
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.../ebi/quickgo/annotation/service/comm/rest/ontology/converter/SlimmingFilterConverter.java
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,62 @@ | ||
| package uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter; | ||
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| import uk.ac.ebi.quickgo.annotation.common.document.AnnotationFields; | ||
| import uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.model.ConvertedOntologyFilter; | ||
| import uk.ac.ebi.quickgo.rest.comm.FilterContext; | ||
| import uk.ac.ebi.quickgo.rest.search.query.QuickGOQuery; | ||
| import uk.ac.ebi.quickgo.rest.search.request.converter.ConvertedFilter; | ||
| import uk.ac.ebi.quickgo.rest.search.request.converter.FilterConverter; | ||
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| import java.util.HashSet; | ||
| import java.util.Set; | ||
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| import static uk.ac.ebi.quickgo.rest.search.query.QuickGOQuery.not; | ||
| import static uk.ac.ebi.quickgo.rest.search.query.QuickGOQuery.or; | ||
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| /** | ||
| * This class is responsible for converting an ontology model containing GO id descendant information, to a | ||
| * {@link ConvertedFilter}. This result encapsulates a {@link QuickGOQuery} applicable to filtering the annotation | ||
| * core data, by these descendants. Additionally, this process records slimming information consisting of original | ||
| * GO ids and their mappings to slimmed up GO ids; this is stored within an instance of {@link SlimmingConversionInfo} | ||
| * available from the {@link ConvertedFilter}'s {@link FilterContext}. | ||
| * | ||
| * Created 09/08/16 | ||
| * @author Edd | ||
| */ | ||
| public class SlimmingFilterConverter implements FilterConverter<ConvertedOntologyFilter, QuickGOQuery> { | ||
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| @Override public ConvertedFilter<QuickGOQuery> transform(ConvertedOntologyFilter response) { | ||
| ConvertedFilter<QuickGOQuery> convertedFilter; | ||
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| SlimmingConversionInfo conversionInfo = new SlimmingConversionInfo(); | ||
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| if (response.getResults() != null && atLeastOneDescendantExists(response)) { | ||
| Set<QuickGOQuery> queries = new HashSet<>(); | ||
| FilterContext context = new FilterContext(); | ||
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| for (ConvertedOntologyFilter.Result result : response.getResults()) { | ||
| for (String desc : result.getDescendants()) { | ||
| queries.add(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc)); | ||
| conversionInfo.addOriginal2SlimmedGOIdMapping(desc, result.getId()); | ||
| } | ||
| } | ||
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| context.save(SlimmingConversionInfo.class, conversionInfo); | ||
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| convertedFilter = new ConvertedFilter<>( | ||
| or(queries.toArray(new QuickGOQuery[queries.size()])), | ||
| context); | ||
| } else { | ||
| convertedFilter = new ConvertedFilter<>(not(QuickGOQuery.createAllQuery())); | ||
| } | ||
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| return convertedFilter; | ||
| } | ||
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| private boolean atLeastOneDescendantExists(ConvertedOntologyFilter response) { | ||
| return response.getResults().stream() | ||
| .filter(r -> !r.getDescendants().isEmpty()) | ||
| .findFirst() | ||
| .isPresent(); | ||
| } | ||
| } |
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154
...uickgo/annotation/service/comm/rest/ontology/descendants/SlimmingFilterConverterTest.java
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,154 @@ | ||
| package uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.descendants; | ||
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| import uk.ac.ebi.quickgo.annotation.common.document.AnnotationFields; | ||
| import uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter.SlimmingConversionInfo; | ||
| import uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter.SlimmingFilterConverter; | ||
| import uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.model.ConvertedOntologyFilter; | ||
| import uk.ac.ebi.quickgo.rest.search.query.QuickGOQuery; | ||
| import uk.ac.ebi.quickgo.rest.search.request.converter.ConvertedFilter; | ||
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| import java.util.ArrayList; | ||
| import java.util.List; | ||
| import java.util.Map; | ||
| import org.junit.Before; | ||
| import org.junit.Test; | ||
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| import static java.util.Arrays.asList; | ||
| import static java.util.Collections.singletonList; | ||
| import static org.hamcrest.MatcherAssert.assertThat; | ||
| import static org.hamcrest.collection.IsMapContaining.hasEntry; | ||
| import static org.hamcrest.core.Is.is; | ||
| import static uk.ac.ebi.quickgo.rest.search.query.QuickGOQuery.not; | ||
| import static uk.ac.ebi.quickgo.rest.search.query.QuickGOQuery.or; | ||
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| /** | ||
| * Created 10/08/16 | ||
| * @author Edd | ||
| */ | ||
| public class SlimmingFilterConverterTest { | ||
| private ConvertedOntologyFilter response; | ||
| private SlimmingFilterConverter converter; | ||
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| @Before | ||
| public void setUp() { | ||
| response = new ConvertedOntologyFilter(); | ||
| response.setResults(new ArrayList<>()); | ||
| converter = new SlimmingFilterConverter(); | ||
| } | ||
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| @Test | ||
| public void descendantsFromSingleResourceAreConvertedToQuickGOQuery() { | ||
| String id1 = "id1"; | ||
| String desc1 = "desc1"; | ||
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| addResponseDescendant(id1, desc1); | ||
| ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response); | ||
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| assertThat(convertedFilter.getConvertedValue(), is(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1))); | ||
| assertThat(convertedFilter.getFilterContext().isPresent(), is(true)); | ||
| } | ||
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| @Test | ||
| public void differentDescendantsFromMultipleResourcesAreConvertedToQuickGOQuery() { | ||
| String id1 = "id1"; | ||
| String id2 = "id2"; | ||
| String desc1 = "desc1"; | ||
| String desc2 = "desc2"; | ||
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| addResponseDescendant(id1, desc1); | ||
| addResponseDescendant(id2, desc2); | ||
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| ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response); | ||
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| assertThat(convertedFilter.getConvertedValue(), is( | ||
| or(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1), | ||
| QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc2)))); | ||
| assertThat(convertedFilter.getFilterContext().isPresent(), is(true)); | ||
| } | ||
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| @Test | ||
| public void sameDescendantsFromMultipleResourcesAreConvertedToQuickGOQuery() { | ||
| String id1 = "id1"; | ||
| String id2 = "id2"; | ||
| String desc1 = "desc1"; | ||
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| addResponseDescendant(id1, desc1); | ||
| addResponseDescendant(id2, desc1); | ||
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| ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response); | ||
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| assertThat(convertedFilter.getConvertedValue(), is( | ||
| QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1))); | ||
| assertThat(convertedFilter.getFilterContext().isPresent(), is(true)); | ||
| } | ||
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| @Test | ||
| public void nullResultsMeansFilterEverything() { | ||
| response.setResults(null); | ||
| ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response); | ||
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| assertThat(convertedFilter.getConvertedValue(), is(not(QuickGOQuery.createAllQuery()))); | ||
| } | ||
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| @Test | ||
| public void emptyResultsMeansFilterEverything() { | ||
| ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response); | ||
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| assertThat(convertedFilter.getConvertedValue(), is(not(QuickGOQuery.createAllQuery()))); | ||
| } | ||
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| @Test | ||
| public void conversionContextContainsOneMapping() { | ||
| String id1 = "id1"; | ||
| String desc1 = "desc1"; | ||
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| addResponseDescendant(id1, desc1); | ||
| ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response); | ||
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| assertThat(extractContextProperties(convertedFilter), hasEntry(desc1, singletonList(id1))); | ||
| } | ||
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| @Test | ||
| public void conversionContextContainsTwoMappings() { | ||
| String id1 = "id1"; | ||
| String id2 = "id2"; | ||
| String desc1 = "desc1"; | ||
| String desc2 = "desc2"; | ||
| String desc3 = "desc3"; | ||
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| addResponseDescendant(id1, desc1); | ||
| addResponseDescendant(id1, desc2); | ||
| addResponseDescendant(id1, desc3); | ||
| addResponseDescendant(id2, desc3); | ||
| ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response); | ||
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| assertThat(extractContextProperties(convertedFilter), hasEntry(desc1, singletonList(id1))); | ||
| assertThat(extractContextProperties(convertedFilter), hasEntry(desc2, singletonList(id1))); | ||
| assertThat(extractContextProperties(convertedFilter), hasEntry(desc3, asList(id1, id2))); | ||
| } | ||
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| private Map<String, List<String>> extractContextProperties(ConvertedFilter<QuickGOQuery> convertedFilter) { | ||
| SlimmingConversionInfo conversionInfo = convertedFilter.getFilterContext() | ||
| .map(t -> t.get(SlimmingConversionInfo.class) | ||
| .orElse(new SlimmingConversionInfo())) | ||
| .orElseThrow(IllegalStateException::new); | ||
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| return conversionInfo.getInfo(); | ||
| } | ||
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| private void addResponseDescendant(String termId, String descendantId) { | ||
| for (ConvertedOntologyFilter.Result result : response.getResults()) { | ||
| if (result.getId().equals(termId)) { | ||
| result.getDescendants().add(descendantId); | ||
| return; | ||
| } | ||
| } | ||
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| ConvertedOntologyFilter.Result newResult = new ConvertedOntologyFilter.Result(); | ||
| newResult.setId(termId); | ||
| List<String> descList = new ArrayList<>(); | ||
| descList.add(descendantId); | ||
| newResult.setDescendants(descList); | ||
| response.getResults().add(newResult); | ||
| } | ||
| } |
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