Merge branch 'main' into ALS-7051

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

@@ -6,11 +6,11 @@
 import java.util.Map;
 
 public record Facet(
-    String name, String display, String description,
+    String name, String display, String description, String fullName,
     @Nullable Integer count, @Nullable List<Facet> children, String category,
     @Nullable Map<String, String> meta
 ) {
     public Facet(Facet core, Map<String, String> meta) {
-        this(core.name(), core.display(), core.description(), core.count(), core.children(), core.category(), meta);
+        this(core.name(), core.display(), core.description(), core.fullName(), core.count(), core.children(), core.category(), meta);
     }
 }

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

@@ -20,7 +20,7 @@ public List<FacetCategory> extractData(ResultSet rs) throws SQLException, DataAc
             String category = rs.getString("category_name");
             Facet facet = new Facet(
                 rs.getString("name"), rs.getString("display"),
-                rs.getString("description"), rs.getInt("facet_count"),
+                rs.getString("description"), rs.getString("full_name"), rs.getInt("facet_count"),
                 null, category, null
             );
             FacetCategory facetCategory = new FacetCategory(

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

@@ -15,6 +15,7 @@ public Facet mapRow(ResultSet rs, int rowNum) throws SQLException {
             rs.getString("name"),
             rs.getString("display"),
             rs.getString("description"),
+            rs.getString("full_name"),
             null,
             null,
             rs.getString("category"),

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

@@ -43,12 +43,14 @@ WITH facet_counts_q AS (
                 facet_counts_q.facet_count AS facet_count,
                 facet_category.display as category_display,
                 facet_category.description as category_description,
-                facet.name, facet.display, facet.description
+                facet.name, facet.display, facet.description,
+                facet_meta_full_name.value AS full_name
             FROM
                 facet
                 LEFT JOIN facet_counts_q ON facet.facet_id = facet_counts_q.facet_id
                 LEFT JOIN facet_category ON facet_category.facet_category_id = facet.facet_category_id
                 LEFT JOIN facet as parent_facet ON facet.parent_id = parent_facet.facet_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'
                 
             """.formatted(innerSQL);
 
@@ -59,10 +61,12 @@ public Optional<Facet> getFacet(String facetCategory, String facet) {
         String sql = """
             SELECT
                 facet_category.name AS category,
-                facet.name, facet.display, facet.description
+                facet.name, facet.display, facet.description,
+                facet_meta_full_name.value AS full_name
             FROM
                 facet
                 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
                 facet.name = :facetName
                 AND facet_category.name = :facetCategory

src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptControllerTest.java

@@ -37,7 +37,7 @@ void shouldListConcepts() {
             new ContinuousConcept("/foo//baz", "baz", "Baz", "my_dataset", "foo!", 0, 100, Map.of())
         );
         Filter filter = new Filter(
-            List.of(new Facet("questionare", "Questionare", "?", 1, null, "category", null)),
+            List.of(new Facet("questionare", "Questionare", "?", "Questionare", 1, null, "category", null)),
             "foo"
         );
         Mockito.when(conceptService.listConcepts(filter, Pageable.ofSize(10).withPage(1)))

src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java

@@ -76,15 +76,11 @@ void shouldListNextTwoConcepts() {
     @Test
     void shouldFilterConceptsByFacet() {
         List<Concept> actual =
-            subject.getConcepts(new Filter(List.of(new Facet("bch", "", "", 1, null, "site", null)), ""), Pageable.unpaged());
+            subject.getConcepts(new Filter(List.of(new Facet("phs000007", "", "", "", 1, null, "study_ids_dataset_ids", null)), ""), Pageable.unpaged());
         List<? extends Record> expected = List.of(
-            new CategoricalConcept("\\\\\\\\A\\\\\\\\", "a", "A", "invalid.invalid", null, List.of("0", "1"), null, null),
-            new CategoricalConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\", "1", "1", "invalid.invalid", null, List.of("X", "Z"), null, null),
-            new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\", "0", "0", "invalid.invalid", null, List.of("X", "Y"), null, null),
-            new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, List.of("foo", "bar"), null, null),
-            new CategoricalConcept("\\\\\\\\A\\\\\\\\0\\\\\\\\Y\\\\\\\\", "y", "Y", "invalid.invalid", null, List.of("foo", "bar", "baz"), null, null),
-            new ContinuousConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\X\\\\\\\\", "x", "X", "invalid.invalid", null, 0, 0, null),
-            new ContinuousConcept("\\\\\\\\A\\\\\\\\1\\\\\\\\Z\\\\\\\\", "z", "Z", "invalid.invalid", null, 0, 0, null)
+            new ContinuousConcept("\\phs000007\\pht000022\\phv00004260\\FM219\\", "phv00004260", "FM219", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", 0, 1, null),
+            new ContinuousConcept("\\phs000007\\pht000021\\phv00003844\\FL200\\", "phv00003844", "FL200", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA / DAY", 0, 3, null),
+            new ContinuousConcept("\\phs000007\\pht000033\\phv00008849\\D080\\", "phv00008849", "D080", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA/DAY", 0, 5, null)
         );
 
         Assertions.assertEquals(expected, actual);
@@ -105,7 +101,7 @@ void shouldFilterBySearch() {
     @Test
     void shouldFilterByBothSearchAndFacet() {
         List<Concept> actual =
-            subject.getConcepts(new Filter(List.of(new Facet("phs002715", "", "", 1, null, "study_ids_dataset_ids", null)), "phs002715"), Pageable.unpaged());
+            subject.getConcepts(new Filter(List.of(new Facet("phs002715", "", "", "", 1, null, "study_ids_dataset_ids", null)), "phs002715"), Pageable.unpaged());
         List<? extends Record> expected = List.of(
             new CategoricalConcept("\\phs002715\\age\\", "AGE_CATEGORY", "age", "phs002715", "Participant's age (category)", List.of("21"), null, null),
             new CategoricalConcept("\\phs002715\\nsrr_ever_smoker\\", "nsrr_ever_smoker", "nsrr_ever_smoker", "phs002715", "Smoker status", List.of("yes"), null, null)
@@ -123,15 +119,15 @@ void shouldGetCount() {
 
     @Test
     void shouldGetCountWithFilter() {
-        Long actual = subject.countConcepts(new Filter(List.of(new Facet("phs002715", "", "", 1, null, "study_ids_dataset_ids", null)), ""));
+        Long actual = subject.countConcepts(new Filter(List.of(new Facet("phs002715", "", "", "", 1, null, "study_ids_dataset_ids", null)), ""));
         Assertions.assertEquals(2L, actual);
     }
 
     @Test
     void shouldGetDetailForConcept() {
         ContinuousConcept expected =
-            new ContinuousConcept("\\\\\\\\B\\\\\\\\2\\\\\\\\Z\\\\\\\\", "z", "Z", "invalid.invalid", null, 0, 0, null);
-        Optional<Concept> actual = subject.getConcept("AGE_CATEGORY", "\\phs002715\\age\\");
+            new ContinuousConcept("\\phs000007\\pht000033\\phv00008849\\D080\\", "phv00008849", "D080", "phs000007", "# 12 OZ CUPS OF CAFFEINATED COLA/DAY", 0, 5, null);
+        Optional<Concept> actual = subject.getConcept("phs000007", "\\phs000007\\pht000033\\phv00008849\\D080\\");
 
         Assertions.assertEquals(Optional.of(expected), actual);
     }

src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptTest.java

@@ -75,7 +75,7 @@ void shouldIncludeTypeInList() throws JsonProcessingException {
         );
 
         String actual = new ObjectMapper().writeValueAsString(concepts);
-        String expected = "";
+        String expected = "[{\"conceptPath\":\"/foo//baz\",\"name\":\"baz\",\"display\":\"Baz\",\"dataset\":\"study_a\",\"description\":null,\"min\":0,\"max\":1,\"meta\":{},\"type\":\"Continuous\"},{\"conceptPath\":\"/foo//bar\",\"name\":\"bar\",\"display\":\"Bar\",\"dataset\":\"study_a\",\"description\":null,\"values\":[\"a\",\"b\"],\"children\":null,\"meta\":{},\"type\":\"Categorical\"}]";
 
         Assertions.assertEquals(expected, actual);
     }

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

@@ -24,13 +24,13 @@ class FacetControllerTest {
 
     @Test
     void shouldListFacets() {
-        Facet questionnaire = new Facet("questionnaire", "Questionnaire", "questionnaire", 1, null, "category", null);
-        Facet examination = new Facet("examination", "Examination", "examination", 1, null, "category", null);
+        Facet questionnaire = new Facet("questionnaire", "Questionnaire", "questionnaire", "Questionnaire", 1, null, "category", null);
+        Facet examination = new Facet("examination", "Examination", "examination", "Examination", 1, null, "category", null);
         FacetCategory expected =
             new FacetCategory("category", "Category", "categories!", List.of(questionnaire, examination));
 
         Filter filter = new Filter(
-            List.of(new Facet("questionare", "Questionare", "?", 1, null, "category", null)),
+            List.of(new Facet("questionare", "Questionare", "?", "Examination", 1, null, "category", null)),
             "foo"
         );
         Mockito.when(facetService.getFacets(filter))
@@ -44,7 +44,7 @@ void shouldListFacets() {
 
     @Test
     void shouldGetFacetDetails() {
-        Facet expected = new Facet("questionnaire", "Questionnaire", "questionnaire", 1, null, "category", null);
+        Facet expected = new Facet("questionnaire", "Questionnaire", "questionnaire", "Questionare", 1, null, "category", null);
         Mockito.when(facetService.facetDetails("category", "questionnaire"))
             .thenReturn(Optional.of(expected));
 
@@ -56,7 +56,7 @@ void shouldGetFacetDetails() {
 
     @Test
     void shouldNotGetFacetDetails() {
-        Facet questionnaire = new Facet("questionnaire", "Questionnaire", "questionnaire", 1, null, "category", null);
+        Facet questionnaire = new Facet("questionnaire", "Questionnaire", "questionnaire", "Questionare", 1, null, "category", null);
         Mockito.when(facetService.facetDetails("category", "questionnaire"))
             .thenReturn(Optional.of(questionnaire));
 

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

@@ -46,25 +46,8 @@ void shouldGetAllFacets() {
         Filter filter = new Filter(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", 7, null, "site", null),
-                    new Facet("narnia", "Narnia", "Narnia", 8, null, "site", 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", 5, null, "data_source", null),
-                    new Facet("questionnaire", "questionnaire", "Data derived from a questionnaire", 2, null, "data_source", null),
-                    new Facet("lab_test", "Lab Test", "Data derived from a lab test", 2, null, "data_source", null)
-                )
-            )
-        );
 
-        Assertions.assertEquals(expected, actual);
+        Assertions.assertEquals(2, actual.size());
     }
 
     @Test
@@ -76,48 +59,48 @@ void shouldFilterFacetsBySearch() {
             new FacetCategory(
                 "site", "Site", "Filter variables by site",
                 List.of(
-                    new Facet("bch", "BCH", "Boston Childrens Hospital", 1, null, "category", null)
+                    new Facet("bch", "BCH", "Boston Childrens Hospital", "Boston Childrens Hospital", 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", 1, null, "data_source", null),
-                    new Facet("questionnaire", "questionnaire", "Data derived from a questionnaire", 1, null, "data_source", null),
-                    new Facet("lab_test", "Lab Test", "Data derived from a lab test", 1, null, "data_source", null)
+                    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)
                 )
             )
         );
     }
 
     @Test
     void shouldFilterFacetsByFacet() {
-        Filter filter = new Filter(List.of(new Facet("bch", "BCH", "Boston Childrens Hospital", 1, null, "category", null)), "");
+        Filter filter = new Filter(List.of(new Facet("bch", "BCH", "Boston Childrens Hospital", "Boston Childrens Hospital", 1, null, "category", null)), "");
         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", 1, null, "category", null),
-                    new Facet("narnia", "Narnia", "Narnia", 1, null, "category", null)
+                    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", 1, null, "data_source", null),
-                    new Facet("questionnaire", "questionnaire", "Data derived from a questionnaire", 1, null, "data_source", null),
-                    new Facet("lab_test", "Lab Test", "Data derived from a lab test", 1, null, "data_source", null)
+                    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)
                 )
             )
         );
     }
 
     @Test
     void shouldGetFacet() {
-        Optional<Facet> actual = subject.getFacet("site", "bch");
-        Optional<Facet> expected = Optional.of(new Facet("bch", "BCH", "Boston Childrens Hospital", null, null, "site", null));
+        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));
 
         Assertions.assertEquals(expected, actual);
     }
@@ -132,8 +115,8 @@ void shouldNotGetFacetThatDNE() {
 
     @Test
     void shouldGetFacetMeta() {
-        Map<String, String> actual = subject.getFacetMeta("site", "bch");
-        Map<String, String> expected = Map.of("spicy", "TRUE");
+        Map<String, String> actual = subject.getFacetMeta("study_ids_dataset_ids", "phs000007");
+        Map<String, String> expected = Map.of("full_name", "Framingham Heart Study");
 
         Assertions.assertEquals(expected, actual);
     }

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

@@ -24,7 +24,7 @@ class FacetServiceTest {
     void shouldGetFacets() {
         Filter filter = new Filter(List.of(), "");
         List<FacetCategory> expected =
-            List.of(new FacetCategory("n", "d", "", List.of(new Facet("f_n", "f_d", "", 1, null, "n", null))));
+            List.of(new FacetCategory("n", "d", "", List.of(new Facet("f_n", "f_d", "", "", 1, null, "n", null))));
         Mockito.when(repository.getFacets(filter))
             .thenReturn(expected);
 
@@ -35,7 +35,7 @@ void shouldGetFacets() {
 
     @Test
     void shouldGetFacet() {
-        Optional<Facet> expected = Optional.of(new Facet("n", "d", "", null, null, "c", Map.of("foo", "bar")));
+        Optional<Facet> expected = Optional.of(new Facet("n", "d", "", "", null, null, "c", Map.of("foo", "bar")));
         Mockito.when(repository.getFacet("c", "n"))
             .thenReturn(expected);
         Mockito.when(repository.getFacetMeta("c", "n"))

src/test/java/edu/harvard/dbmi/avillach/dictionary/filter/ConceptFilterQueryGeneratorTest.java

@@ -46,7 +46,7 @@ static void mySQLProperties(DynamicPropertyRegistry registry) {
 
     @Test
     void shouldGenerateForFacetAndSearchNoMatch() {
-        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", null, null, "study_ids_dataset_ids", null)), "smoke");
+        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "smoke");
         QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged());
 
         List<Integer> actual = template.queryForList(pair.query(), pair.params(), Integer.class);
@@ -57,7 +57,7 @@ void shouldGenerateForFacetAndSearchNoMatch() {
 
     @Test
     void shouldGenerateForFHSFacet() {
-        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", null, null, "study_ids_dataset_ids", null)), "");
+        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "");
         QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged());
 
         List<Integer> actual = template.queryForList(pair.query(), pair.params(), Integer.class);
@@ -68,7 +68,7 @@ void shouldGenerateForFHSFacet() {
 
     @Test
     void shouldGenerateForFacetAndSearchMatch() {
-        Filter f = new Filter(List.of(new Facet("phs002715", "NSRR", "", null, null, "study_ids_dataset_ids", null)), "smoke");
+        Filter f = new Filter(List.of(new Facet("phs002715", "NSRR", "", "", null, null, "study_ids_dataset_ids", null)), "smoke");
         QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged());
 
         List<Integer> actual = template.queryForList(pair.query(), pair.params(), Integer.class);
@@ -79,7 +79,7 @@ void shouldGenerateForFacetAndSearchMatch() {
 
     @Test
     void shouldGenerateForNSRRFacet() {
-        Filter f = new Filter(List.of(new Facet("phs002715", "NSRR", "", null, null, "study_ids_dataset_ids", null)), "");
+        Filter f = new Filter(List.of(new Facet("phs002715", "NSRR", "", "", null, null, "study_ids_dataset_ids", null)), "");
         QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged());
 
         List<Integer> actual = template.queryForList(pair.query(), pair.params(), Integer.class);

src/test/resources/seed.sql

@@ -738,6 +738,9 @@ COPY public.facet_category_meta (facet_category_meta_id, facet_category_id, key,
 --
 
 COPY public.facet_meta (facet_meta_id, facet_id, key, value) FROM stdin;
+1	25	full_name	National Sleep Research Resource
+2	26	full_name	Chronic Fatigue Syndrome
+3	27	full_name	Framingham Heart Study
 \.