ebi-uniprot · eddturner · Aug 24, 2016 · Aug 24, 2016
diff --git a/...i/quickgo/annotation/service/comm/rest/ontology/converter/DescendantsFilterConverter.java b/...i/quickgo/annotation/service/comm/rest/ontology/converter/DescendantsFilterConverter.java
@@ -2,7 +2,6 @@
 
 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;
@@ -16,9 +15,7 @@
 /**
  * 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}.
+ * core data, by these descendants.
  *
  * Created 09/08/16
  * @author Edd
@@ -28,24 +25,16 @@ public class DescendantsFilterConverter implements FilterConverter<ConvertedOnto
     @Override public ConvertedFilter<QuickGOQuery> transform(ConvertedOntologyFilter response) {
         ConvertedFilter<QuickGOQuery> convertedFilter;
 
-        SlimmingConversionInfo conversionInfo = new SlimmingConversionInfo();
-
         if (response.getResults() != null && atLeastOneDescendantExists(response)) {
             Set<QuickGOQuery> queries = new HashSet<>();
-            FilterContext context = new FilterContext();
 
             for (ConvertedOntologyFilter.Result result : response.getResults()) {
                 for (String desc : result.getDescendants()) {
                     queries.add(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc));
-                    conversionInfo.addOriginal2SlimmedGOIdMapping(desc, result.getId());
                 }
             }
 
-            context.save(SlimmingConversionInfo.class, conversionInfo);
-
-            convertedFilter = new ConvertedFilter<>(
-                    or(queries.toArray(new QuickGOQuery[queries.size()])),
-                    context);
+            convertedFilter = new ConvertedFilter<>(or(queries.toArray(new QuickGOQuery[queries.size()])));
         } else {
             convertedFilter = new ConvertedFilter<>(not(QuickGOQuery.createAllQuery()));
         }

diff --git a/.../ebi/quickgo/annotation/service/comm/rest/ontology/converter/SlimmingFilterConverter.java b/.../ebi/quickgo/annotation/service/comm/rest/ontology/converter/SlimmingFilterConverter.java
@@ -0,0 +1,62 @@
+package uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter;
+
+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;
+
+import java.util.HashSet;
+import java.util.Set;
+
+import static uk.ac.ebi.quickgo.rest.search.query.QuickGOQuery.not;
+import static uk.ac.ebi.quickgo.rest.search.query.QuickGOQuery.or;
+
+/**
+ * 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> {
+
+    @Override public ConvertedFilter<QuickGOQuery> transform(ConvertedOntologyFilter response) {
+        ConvertedFilter<QuickGOQuery> convertedFilter;
+
+        SlimmingConversionInfo conversionInfo = new SlimmingConversionInfo();
+
+        if (response.getResults() != null && atLeastOneDescendantExists(response)) {
+            Set<QuickGOQuery> queries = new HashSet<>();
+            FilterContext context = new FilterContext();
+
+            for (ConvertedOntologyFilter.Result result : response.getResults()) {
+                for (String desc : result.getDescendants()) {
+                    queries.add(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc));
+                    conversionInfo.addOriginal2SlimmedGOIdMapping(desc, result.getId());
+                }
+            }
+
+            context.save(SlimmingConversionInfo.class, conversionInfo);
+
+            convertedFilter = new ConvertedFilter<>(
+                    or(queries.toArray(new QuickGOQuery[queries.size()])),
+                    context);
+        } else {
+            convertedFilter = new ConvertedFilter<>(not(QuickGOQuery.createAllQuery()));
+        }
+
+        return convertedFilter;
+    }
+
+    private boolean atLeastOneDescendantExists(ConvertedOntologyFilter response) {
+        return response.getResults().stream()
+                .filter(r -> !r.getDescendants().isEmpty())
+                .findFirst()
+                .isPresent();
+    }
+}
diff --git a/...kgo/annotation/service/comm/rest/ontology/descendants/DescendantsFilterConverterTest.java b/...kgo/annotation/service/comm/rest/ontology/descendants/DescendantsFilterConverterTest.java
@@ -2,21 +2,17 @@
 
 import uk.ac.ebi.quickgo.annotation.common.document.AnnotationFields;
 import uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter.DescendantsFilterConverter;
-import uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter.SlimmingConversionInfo;
 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;
 
 import java.util.ArrayList;
 import java.util.List;
-import java.util.Map;
+import java.util.Optional;
 import org.junit.Before;
 import org.junit.Test;
 
-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;
@@ -45,6 +41,7 @@ public void descendantsFromSingleResourceAreConvertedToQuickGOQuery() {
         ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
 
         assertThat(convertedFilter.getConvertedValue(), is(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1)));
+        assertThat(convertedFilter.getFilterContext(), is(Optional.empty()));
     }
 
     @Test
@@ -62,6 +59,7 @@ public void differentDescendantsFromMultipleResourcesAreConvertedToQuickGOQuery(
         assertThat(convertedFilter.getConvertedValue(), is(
                 or(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1),
                         QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc2))));
+        assertThat(convertedFilter.getFilterContext(), is(Optional.empty()));
     }
 
     @Test
@@ -77,6 +75,7 @@ public void sameDescendantsFromMultipleResourcesAreConvertedToQuickGOQuery() {
 
         assertThat(convertedFilter.getConvertedValue(), is(
                 QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1)));
+        assertThat(convertedFilter.getFilterContext(), is(Optional.empty()));
     }
 
     @Test
@@ -85,52 +84,15 @@ public void nullResultsMeansFilterEverything() {
         ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
 
         assertThat(convertedFilter.getConvertedValue(), is(not(QuickGOQuery.createAllQuery())));
+        assertThat(convertedFilter.getFilterContext(), is(Optional.empty()));
     }
 
     @Test
     public void emptyResultsMeansFilterEverything() {
         ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
 
         assertThat(convertedFilter.getConvertedValue(), is(not(QuickGOQuery.createAllQuery())));
-    }
-
-    @Test
-    public void conversionContextContainsOneMapping() {
-        String id1 = "id1";
-        String desc1 = "desc1";
-
-        addResponseDescendant(id1, desc1);
-        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
-
-        assertThat(extractContextProperties(convertedFilter), hasEntry(desc1, singletonList(id1)));
-    }
-
-    @Test
-    public void conversionContextContainsTwoMappings() {
-        String id1 = "id1";
-        String id2 = "id2";
-        String desc1 = "desc1";
-        String desc2 = "desc2";
-        String desc3 = "desc3";
-
-        addResponseDescendant(id1, desc1);
-        addResponseDescendant(id1, desc2);
-        addResponseDescendant(id1, desc3);
-        addResponseDescendant(id2, desc3);
-        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
-
-        assertThat(extractContextProperties(convertedFilter), hasEntry(desc1, singletonList(id1)));
-        assertThat(extractContextProperties(convertedFilter), hasEntry(desc2, singletonList(id1)));
-        assertThat(extractContextProperties(convertedFilter), hasEntry(desc3, asList(id1, id2)));
-    }
-
-    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);
-
-        return conversionInfo.getInfo();
+        assertThat(convertedFilter.getFilterContext(), is(Optional.empty()));
     }
 
     private void addResponseDescendant(String termId, String descendantId) {

diff --git a/...uickgo/annotation/service/comm/rest/ontology/descendants/SlimmingFilterConverterTest.java b/...uickgo/annotation/service/comm/rest/ontology/descendants/SlimmingFilterConverterTest.java
@@ -0,0 +1,154 @@
+package uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.descendants;
+
+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;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+import org.junit.Before;
+import org.junit.Test;
+
+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;
+
+/**
+ * Created 10/08/16
+ * @author Edd
+ */
+public class SlimmingFilterConverterTest {
+    private ConvertedOntologyFilter response;
+    private SlimmingFilterConverter converter;
+
+    @Before
+    public void setUp() {
+        response = new ConvertedOntologyFilter();
+        response.setResults(new ArrayList<>());
+        converter = new SlimmingFilterConverter();
+    }
+
+    @Test
+    public void descendantsFromSingleResourceAreConvertedToQuickGOQuery() {
+        String id1 = "id1";
+        String desc1 = "desc1";
+
+        addResponseDescendant(id1, desc1);
+        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
+
+        assertThat(convertedFilter.getConvertedValue(), is(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1)));
+        assertThat(convertedFilter.getFilterContext().isPresent(), is(true));
+    }
+
+    @Test
+    public void differentDescendantsFromMultipleResourcesAreConvertedToQuickGOQuery() {
+        String id1 = "id1";
+        String id2 = "id2";
+        String desc1 = "desc1";
+        String desc2 = "desc2";
+
+        addResponseDescendant(id1, desc1);
+        addResponseDescendant(id2, desc2);
+
+        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
+
+        assertThat(convertedFilter.getConvertedValue(), is(
+                or(QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1),
+                        QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc2))));
+        assertThat(convertedFilter.getFilterContext().isPresent(), is(true));
+    }
+
+    @Test
+    public void sameDescendantsFromMultipleResourcesAreConvertedToQuickGOQuery() {
+        String id1 = "id1";
+        String id2 = "id2";
+        String desc1 = "desc1";
+
+        addResponseDescendant(id1, desc1);
+        addResponseDescendant(id2, desc1);
+
+        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
+
+        assertThat(convertedFilter.getConvertedValue(), is(
+                QuickGOQuery.createQuery(AnnotationFields.GO_ID, desc1)));
+        assertThat(convertedFilter.getFilterContext().isPresent(), is(true));
+    }
+
+    @Test
+    public void nullResultsMeansFilterEverything() {
+        response.setResults(null);
+        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
+
+        assertThat(convertedFilter.getConvertedValue(), is(not(QuickGOQuery.createAllQuery())));
+    }
+
+    @Test
+    public void emptyResultsMeansFilterEverything() {
+        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
+
+        assertThat(convertedFilter.getConvertedValue(), is(not(QuickGOQuery.createAllQuery())));
+    }
+
+    @Test
+    public void conversionContextContainsOneMapping() {
+        String id1 = "id1";
+        String desc1 = "desc1";
+
+        addResponseDescendant(id1, desc1);
+        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
+
+        assertThat(extractContextProperties(convertedFilter), hasEntry(desc1, singletonList(id1)));
+    }
+
+    @Test
+    public void conversionContextContainsTwoMappings() {
+        String id1 = "id1";
+        String id2 = "id2";
+        String desc1 = "desc1";
+        String desc2 = "desc2";
+        String desc3 = "desc3";
+
+        addResponseDescendant(id1, desc1);
+        addResponseDescendant(id1, desc2);
+        addResponseDescendant(id1, desc3);
+        addResponseDescendant(id2, desc3);
+        ConvertedFilter<QuickGOQuery> convertedFilter = converter.transform(response);
+
+        assertThat(extractContextProperties(convertedFilter), hasEntry(desc1, singletonList(id1)));
+        assertThat(extractContextProperties(convertedFilter), hasEntry(desc2, singletonList(id1)));
+        assertThat(extractContextProperties(convertedFilter), hasEntry(desc3, asList(id1, id2)));
+    }
+
+    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);
+
+        return conversionInfo.getInfo();
+    }
+
+    private void addResponseDescendant(String termId, String descendantId) {
+        for (ConvertedOntologyFilter.Result result : response.getResults()) {
+            if (result.getId().equals(termId)) {
+                result.getDescendants().add(descendantId);
+                return;
+            }
+        }
+
+        ConvertedOntologyFilter.Result newResult = new ConvertedOntologyFilter.Result();
+        newResult.setId(termId);
+        List<String> descList = new ArrayList<>();
+        descList.add(descendantId);
+        newResult.setDescendants(descList);
+        response.getResults().add(newResult);
+    }
+}
diff --git a/annotation-rest/src/test/resources/application.yml b/annotation-rest/src/test/resources/application.yml
@@ -21,7 +21,7 @@ search:
           ip: localhost,
           resourceFormat: "/QuickGO/services/go/terms/{usageIds}/descendants?relations={usageRelationships}",
           responseClass: "uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.model.ConvertedOntologyFilter",
-          responseConverter: "uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter.DescendantsFilterConverter"
+          responseConverter: "uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter.SlimmingFilterConverter"
         }
 model:
   repo2domainFieldNameTransformations:

diff --git a/deployments/src/main/distros/rest/bin/annotation/application.yml b/deployments/src/main/distros/rest/bin/annotation/application.yml
@@ -21,7 +21,7 @@ search:
           ip: "http://ves-hx-c2:8082",
           resourceFormat: "/QuickGO/services/go/terms/{usageIds}/descendants?relations={usageRelationships}",
           responseClass: "uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.model.ConvertedOntologyFilter",
-          responseConverter: "uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter.DescendantsFilterConverter"
+          responseConverter: "uk.ac.ebi.quickgo.annotation.service.comm.rest.ontology.converter.SlimmingFilterConverter"
         }
 model:
   repo2domainFieldNameTransformations: