[ALS-7466] Harmony among consents

hms-dbmi · Oct 1, 2024 · 070c0cd · 070c0cd
1 parent 9d0a770
commit 070c0cd
Show file tree

Hide file tree

Showing 6 changed files with 52 additions and 2 deletions.
diff --git a/db/schema.sql b/db/schema.sql
@@ -105,6 +105,7 @@ CREATE TABLE dict.facet__concept_node (
     CONSTRAINT fk_facet FOREIGN KEY (FACET_ID) REFERENCES dict.facet(FACET_ID),
     CONSTRAINT fk_concept_node FOREIGN KEY (CONCEPT_NODE_ID) REFERENCES dict.concept_node(CONCEPT_NODE_ID)
 );
+
 CREATE TABLE IF NOT EXISTS dict.dataset_harmonization
 (
     dataset_harmonization_id INT NOT NULL GENERATED BY DEFAULT AS IDENTITY,

diff --git a/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptFilterQueryGenerator.java b/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptFilterQueryGenerator.java
@@ -24,6 +24,15 @@ dataset.dataset_id IN (
                     WHERE
                         concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR
                         (dataset.ref IN (:consents) AND consent.consent_code = '')
+                    UNION
+                    SELECT
+                        dataset_harmonization.harmonized_dataset_id
+                    FROM consent
+                        JOIN dataset_harmonization ON dataset_harmonization.source_dataset_id = consent.dataset_id
+                        LEFT JOIN dataset ON dataset.dataset_id = dataset_harmonization.source_dataset_id
+                    WHERE
+                        concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR
+                        (dataset.ref IN (:consents) AND consent.consent_code = '')
                 ) AND
                 """;
 

diff --git a/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGenerator.java b/src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGenerator.java
@@ -24,6 +24,15 @@ dataset.dataset_id IN (
                     WHERE
                         concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR
                         (dataset.ref IN (:consents) AND consent.consent_code = '')
+                    UNION
+                    SELECT
+                        dataset_harmonization.harmonized_dataset_id
+                    FROM consent
+                        JOIN dataset_harmonization ON dataset_harmonization.source_dataset_id = consent.dataset_id
+                        LEFT JOIN dataset ON dataset.dataset_id = dataset_harmonization.source_dataset_id
+                    WHERE
+                        concat(dataset.ref, '.', consent.consent_code) IN (:consents) OR
+                        (dataset.ref IN (:consents) AND consent.consent_code = '')
                 ) AND
                 """;
 

diff --git a/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java b/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java
@@ -49,7 +49,7 @@ static void mySQLProperties(DynamicPropertyRegistry registry) {
     void shouldListAllConcepts() {
         List<Concept> actual = subject.getConcepts(new Filter(List.of(), "", List.of()), Pageable.unpaged());
 
-        Assertions.assertEquals(29, actual.size());
+        Assertions.assertEquals(30, actual.size());
     }
 
     @Test
@@ -115,7 +115,7 @@ void shouldFilterByBothSearchAndFacet() {
     void shouldGetCount() {
         long actual = subject.countConcepts(new Filter(List.of(), "", List.of()));
 
-        Assertions.assertEquals(29L, actual);
+        Assertions.assertEquals(30L, actual);
     }
 
     @Test

diff --git a/...est/java/edu/harvard/dbmi/avillach/dictionary/filter/ConceptFilterQueryGeneratorTest.java b/...est/java/edu/harvard/dbmi/avillach/dictionary/filter/ConceptFilterQueryGeneratorTest.java
@@ -44,6 +44,17 @@ static void mySQLProperties(DynamicPropertyRegistry registry) {
     @Autowired
     NamedParameterJdbcTemplate template;
 
+    @Test
+    void shouldGenerateForHarmonizedConsents() {
+        Filter filter = new Filter(List.of(), "", List.of("phs001963.c1"));
+        QueryParamPair pair = subject.generateFilterQuery(filter, Pageable.unpaged());
+
+        List<Integer> actual = template.queryForList(pair.query(), pair.params(), Integer.class);
+        List<Integer> expected = List.of(270);
+
+        Assertions.assertEquals(expected, actual);
+    }
+
     @Test
     void shouldGenerateForFacetAndSearchNoMatch() {
         Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "smoke", List.of());

diff --git a/src/test/resources/seed.sql b/src/test/resources/seed.sql
@@ -395,6 +395,7 @@ COPY public.concept_node (concept_node_id, dataset_id, name, display, concept_ty
 267	14	Low coverage WGS	Low coverage WGS	categorical	\\Variant Data Type\\Low coverage WGS\\	265	'coverag':5,8,11 'data':2 'low':4,7,10 'true':13 'type':3 'variant':1 'wgs':6,9,12
 268	14	WES	WES	categorical	\\Variant Data Type\\WES\\	265	'data':2 'exom':7 'sequenc':8 'true':9 'type':3 'variant':1 'wes':4,5 'whole':6
 269	14	WGS	WGS	categorical	\\Variant Data Type\\WGS\\	265	'data':2 'genom':7 'sequenc':8 'true':9 'type':3 'variant':1 'wgs':4,5 'whole':6
+270	26	harmonized_var	harmonized_var	continuous	\\phs003566\\harmonized_var\\	263	'ecgsamplebas':5,8 'origin':4,7 'phs003566':1 'visit01':2,3,6
 \.
 
 
@@ -518,6 +519,7 @@ COPY public.concept_node_meta (concept_node_meta_id, concept_node_id, key, value
 133	211	values	[100, 500]
 36	222	values	[0, 150]
 66	242	values	[0, 30]
+134	270	values	[0, 21]
 \.
 
 
@@ -556,6 +558,7 @@ COPY public.dataset (dataset_id, ref, full_name, abbreviation, description) FROM
 23	phs002808	Nulliparous Pregnancy Outcomes Study: Monitoring Mothers-to-be Heart Health Study (nuMoM2b Heart Health Study)	nuMoM2b	
 24	phs003566	Systolic Blood Pressure Intervention Trial (SPRINT-Imaging)	SPRINT	
 25	phs001963	DEMENTIA-SEQ: WGS in Lewy Body Dementia and Frontotemporal Dementia	DEMENTIA-SEQ	
+26	harmonized	My Cool Harmonized Dataset	abv	harmony
 \.
 
 
@@ -1052,6 +1055,23 @@ ALTER TABLE ONLY public.concept_node
     ADD CONSTRAINT fk_study FOREIGN KEY (dataset_id) REFERENCES public.dataset(dataset_id);
 
 
+CREATE TABLE IF NOT EXISTS public.dataset_harmonization
+(
+    dataset_harmonization_id INT NOT NULL GENERATED BY DEFAULT AS IDENTITY,
+    harmonized_dataset_id INT NOT NULL,
+    source_dataset_id INT NOT NULL,
+    UNIQUE (harmonized_dataset_id, source_dataset_id),
+    CONSTRAINT fk_harmonized_dataset_id FOREIGN KEY (harmonized_dataset_id) REFERENCES public.dataset (dataset_id),
+    CONSTRAINT fk_source_dataset_id FOREIGN KEY (source_dataset_id) REFERENCES public.dataset (dataset_id)
+);
+
+INSERT INTO public.dataset_harmonization (dataset_harmonization_id, harmonized_dataset_id, source_dataset_id) VALUES
+    (1, 26, 25),
+    (1, 26, 24),
+    (1, 26, 23),
+    (1, 26, 22);
+
+
 --
 -- PostgreSQL database dump complete
 --