[ALS-6724] Nested facets

- Nested queries, just 1 level deep for now
- Update details endpoint
- Tests!
- Deleted unused equals fn

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptResultSetExtractor.java

@@ -16,20 +16,7 @@ public class ConceptResultSetExtractor implements ResultSetExtractor<Concept> {
     @Autowired
     private ConceptResultSetUtil conceptResultSetUtil;
 
-    private record ConceptWithId(Concept c, int id) {
-        @Override
-        public boolean equals(Object object) {
-            if (this == object) return true;
-            if (object == null || getClass() != object.getClass()) return false;
-            ConceptWithId conceptWithId = (ConceptWithId) object;
-            return id == conceptWithId.id;
-        }
-
-        @Override
-        public int hashCode() {
-            return Objects.hashCode(id);
-        }
-    };
+    private record ConceptWithId(Concept c, int id) {};
 
     @Override
     public Concept extractData(ResultSet rs) throws SQLException, DataAccessException {

src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/Facet.java

@@ -17,4 +17,8 @@ public Facet(Facet core, Map<String, String> meta) {
     public Facet(String name, String category) {
         this(name, "", "", "", null, null, category, null);
     }
+
+    public Facet withChildren(List<Facet> children) {
+        return new Facet(this.name, this.display, this.description, this.fullName, this.count, children, this.category, this.meta);
+    }
 }

src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetCategoryExtractor.java

@@ -2,6 +2,7 @@
 
 import org.springframework.dao.DataAccessException;
 import org.springframework.jdbc.core.ResultSetExtractor;
+import org.springframework.util.StringUtils;
 
 import java.sql.ResultSet;
 import java.sql.SQLException;
@@ -10,26 +11,44 @@
 
 public class FacetCategoryExtractor implements ResultSetExtractor<List<FacetCategory>> {
 
+    private record Pair(String parent, String category) {
+        Pair(Facet facet) {
+            this(facet.name(), facet.category());
+        }
+    };
+
     @Override
     public List<FacetCategory> extractData(ResultSet rs) throws SQLException, DataAccessException {
         List<Facet> facets = new ArrayList<>();
         Map<String, FacetCategory> categories = new HashMap<>();
+        Map<Pair, List<Facet>> childrenForParent = new HashMap<>();
 
         while (rs.next()) {
             // build out all the facets and make shells of the facet categories
             String category = rs.getString("category_name");
             Facet facet = new Facet(
                 rs.getString("name"), rs.getString("display"),
                 rs.getString("description"), rs.getString("full_name"), rs.getInt("facet_count"),
-                null, category, null
+                List.of(), category, null
             );
             FacetCategory facetCategory = new FacetCategory(
                 category, rs.getString("category_display"),
                 rs.getString("category_description"), List.of()
             );
-            facets.add(facet);
+            String parentName = rs.getString("parent_name");
+            if (StringUtils.hasLength(parentName)) {
+                Pair key = new Pair(parentName, category);
+                List<Facet> facetsForParent = childrenForParent.getOrDefault(key, new ArrayList<>());
+                facetsForParent.add(facet);
+                childrenForParent.put(key, facetsForParent);
+            } else {
+                facets.add(facet);
+            }
             categories.put(category, facetCategory);
         }
+        facets = facets.stream()
+            .map(f -> f.withChildren(childrenForParent.getOrDefault(new Pair(f), List.of())))
+            .toList();
         // group facets by category, then add them to their respective category
         Map<String, List<Facet>> grouped = facets.stream().collect(Collectors.groupingBy(Facet::category));
         return categories.entrySet().stream()

src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetMapper.java

@@ -17,7 +17,7 @@ public Facet mapRow(ResultSet rs, int rowNum) throws SQLException {
             rs.getString("description"),
             rs.getString("full_name"),
             null,
-            null,
+            List.of(),
             rs.getString("category"),
             null
         );

src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetRepository.java

@@ -74,7 +74,29 @@ public Optional<Facet> getFacet(String facetCategory, String facet) {
         MapSqlParameterSource params = new MapSqlParameterSource()
             .addValue("facetCategory", facetCategory)
             .addValue("facetName", facet);
-        return template.query(sql, params, mapper).stream().findFirst();
+        return template.query(sql, params, mapper).stream().findFirst()
+            .map(f -> f.withChildren(getFacetChildren(f.category(), f.name())));
+    }
+
+    private List<Facet> getFacetChildren(String facetCategory, String parentFacetName) {
+        String sql = """
+            SELECT
+                facet_category.name AS category,
+                facet.name, facet.display, facet.description,
+                facet_meta_full_name.value AS full_name
+            FROM
+                facet
+                LEFT JOIN facet as parent_facet ON facet.parent_id = parent_facet.facet_id
+                LEFT JOIN facet_category ON facet_category.facet_category_id = facet.facet_category_id
+                LEFT JOIN facet_meta AS facet_meta_full_name ON facet.facet_id = facet_meta_full_name.facet_id AND facet_meta_full_name.KEY = 'full_name'
+            WHERE
+                parent_facet.name = :facetName
+                AND facet_category.name = :facetCategory
+            """;
+        MapSqlParameterSource params = new MapSqlParameterSource()
+            .addValue("facetCategory", facetCategory)
+            .addValue("facetName", parentFacetName);
+        return template.query(sql, params, mapper);
     }
 
     public Map<String, String> getFacetMeta(String facetCategory, String facet) {

src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetRepositoryTest.java

@@ -44,63 +44,56 @@ static void mySQLProperties(DynamicPropertyRegistry registry) {
     @Test
     void shouldGetAllFacets() {
         Filter filter = new Filter(List.of(), "", List.of());
-
-        List<FacetCategory> actual = subject.getFacets(filter);
-
-        Assertions.assertEquals(2, actual.size());
-    }
-
-    @Test
-    void shouldFilterFacetsBySearch() {
-        Filter filter = new Filter(List.of(), "X", List.of());
         List<FacetCategory> actual = subject.getFacets(filter);
-
         List<FacetCategory> expected = List.of(
-            new FacetCategory(
-                "site", "Site", "Filter variables by site",
+            new FacetCategory("study_ids_dataset_ids", "Study IDs/Dataset IDs", "",
                 List.of(
-                    new Facet("bch", "BCH", "Boston Childrens Hospital", "Boston Childrens Hospital", 1, null, "category", null)
+                    new Facet("1", "GIC", null, null, 13, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs000284", "CFS", null, "Chronic Fatigue Syndrome", 3, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs000007", "FHS", null, "Framingham Heart Study", 3, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs002385", "HCT_for_SCD", null, null, 3, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs002808", "nuMoM2b", null, null, 3, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("2", "National Health and Nutrition Examination Survey", null, null, 2, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs002715", "NSRR CFS", null, "National Sleep Research Resource", 2, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("3", "1000 Genomes Project", null, null, 0, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs003463", "RECOVER_Adult", null, null, 0, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs003543", "NSRR_HSHC", null, null, 0, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs003566", "SPRINT", null, null, 0, List.of(), "study_ids_dataset_ids", null),
+                    new Facet("phs001963", "DEMENTIA-SEQ", null, null, 0, List.of(
+                        new Facet("NEST_1", "My Nested Facet 1", null, null, 0, List.of(), "study_ids_dataset_ids", null),
+                        new Facet("NEST_2", "My Nested Facet 2", null, null, 0, List.of(), "study_ids_dataset_ids", null)
+                    ), "study_ids_dataset_ids", null)
                 )
             ),
-            new FacetCategory(
-                "data_source", "Data Source", "What does this data relate to (image, questionnaire...)",
+            new FacetCategory("nsrr_harmonized", "Common Data Element Collection", "",
                 List.of(
-                    new Facet("imaging", "Imaging", "Data derived from an image", "Data derived from an image", 1, null, "data_source", null),
-                    new Facet("questionnaire", "questionnaire", "Data derived from a questionnaire", "Data derived from a questionnaire", 1, null, "data_source", null),
-                    new Facet("lab_test", "Lab Test", "Data derived from a lab test", "Data derived from a lab test", 1, null, "data_source", null)
+                    new Facet("LOINC", "LOINC", null, null, 1, List.of(), "nsrr_harmonized", null),
+                    new Facet("PhenX", "PhenX", null, null, 1, List.of(), "nsrr_harmonized", null),
+                    new Facet("gad_7", "Generalized Anxiety Disorder Assessment (GAD-7)", null, null, 0, List.of(), "nsrr_harmonized", null),
+                    new Facet("taps_tool", "NIDA CTN Common Data Elements = TAPS Tool", null, null, 0, List.of(), "nsrr_harmonized", null)
                 )
             )
         );
+
+        Assertions.assertEquals(expected, actual);
     }
 
     @Test
-    void shouldFilterFacetsByFacet() {
-        Filter filter = new Filter(List.of(new Facet("bch", "BCH", "Boston Childrens Hospital", "Boston Childrens Hospital", 1, null, "category", null)), "", List.of());
-        List<FacetCategory> actual = subject.getFacets(filter);
-
-        List<FacetCategory> expected = List.of(
-            new FacetCategory(
-                "site", "Site", "Filter variables by site",
-                List.of(
-                    new Facet("bch", "BCH", "Boston Childrens Hospital", "Boston Childrens Hospital", 1, null, "category", null),
-                    new Facet("narnia", "Narnia", "Narnia", "Narnia", 1, null, "category", null)
-                )
-            ),
-            new FacetCategory(
-                "data_source", "Data Source", "What does this data relate to (image, questionnaire...)",
-                List.of(
-                    new Facet("imaging", "Imaging", "Data derived from an image", "Data derived from an image", 1, null, "data_source", null),
-                    new Facet("questionnaire", "questionnaire", "Data derived from a questionnaire", "Data derived from a questionnaire", 1, null, "data_source", null),
-                    new Facet("lab_test", "Lab Test", "Data derived from a lab test", "Data derived from a lab test", 1, null, "data_source", null)
-                )
-            )
-        );
+    void shouldGetFacetWithChildren() {
+        Optional<Facet> actual = subject.getFacet("study_ids_dataset_ids", "phs001963");
+        Facet expected = new Facet("phs001963", "DEMENTIA-SEQ", null, null, null, List.of(
+            new Facet("NEST_1", "My Nested Facet 1", null, null, null, List.of(), "study_ids_dataset_ids", null),
+            new Facet("NEST_2", "My Nested Facet 2", null, null, null, List.of(), "study_ids_dataset_ids", null)
+        ), "study_ids_dataset_ids", null);
+
+        Assertions.assertTrue(actual.isPresent());
+        Assertions.assertEquals(expected, actual.get());
     }
 
     @Test
     void shouldGetFacet() {
         Optional<Facet> actual = subject.getFacet("study_ids_dataset_ids", "phs000007");
-        Optional<Facet> expected = Optional.of(new Facet("phs000007", "FHS", null, "Framingham Heart Study", null, null, "study_ids_dataset_ids", null));
+        Optional<Facet> expected = Optional.of(new Facet("phs000007", "FHS", null, "Framingham Heart Study", null, List.of(), "study_ids_dataset_ids", null));
 
         Assertions.assertEquals(expected, actual);
     }

src/test/resources/seed.sql

@@ -608,6 +608,8 @@ COPY public.facet (facet_id, facet_category_id, name, display, description, pare
 31	1	phs002808	nuMoM2b	\N	\N
 32	1	phs003566	SPRINT	\N	\N
 33	1	phs001963	DEMENTIA-SEQ	\N	\N
+55	1	NEST_1	My Nested Facet 1	\N	33
+56	1	NEST_2	My Nested Facet 2	\N	33
 19	2	gad_7	Generalized Anxiety Disorder Assessment (GAD-7)	\N	\N
 18	2	taps_tool	NIDA CTN Common Data Elements = TAPS Tool	\N	\N
 \.