[CHORE] Now they tell me about the consents. smh

hms-dbmi · Sep 17, 2024 · a622b80 · a622b80
1 parent abf9fe4
commit a622b80
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Showing 4 changed files with 24 additions and 13 deletions.
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
@@ -17,9 +17,13 @@ public class ConceptFilterQueryGenerator {
 
     private static final String CONSENT_QUERY = """
                 dataset.dataset_id IN (
-                    SELECT consent.dataset_id
+                    SELECT
+                        consent.dataset_id
                     FROM consent
-                    WHERE consent.consent_code IN (:consents)
+                        LEFT JOIN dataset ON dataset.dataset_id = consent.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
@@ -17,9 +17,13 @@ public class FacetQueryGenerator {
 
     private static final String CONSENT_QUERY = """
                 dataset.dataset_id IN (
-                    SELECT consent.dataset_id
+                    SELECT
+                        consent.dataset_id
                     FROM consent
-                    WHERE consent.consent_code IN (:consents)
+                        LEFT JOIN dataset ON dataset.dataset_id = consent.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/facet/FacetQueryGeneratorTest.java b/src/test/java/edu/harvard/dbmi/avillach/dictionary/facet/FacetQueryGeneratorTest.java
@@ -74,7 +74,7 @@ void shouldCountFacetsWithNoSearchAndNoSelectedFacetsAndNoConsents() {
 
     @Test
     void shouldCountFacetsWithNoSearchAndNoSelectedFacetsAndConsents() {
-        Filter filter = new Filter(List.of(), "", List.of("c2"));
+        Filter filter = new Filter(List.of(), "", List.of("LOINC.c2", "PhenX.c2", "phs000007.c2"));
 
         MapSqlParameterSource params = new MapSqlParameterSource();
         String query = subject.createFacetSQLAndPopulateParams(filter, params);
@@ -107,7 +107,7 @@ void shouldCountFacetsWithSearchAndNoSelectedFacetsAndNoConsents() {
 
     @Test
     void shouldCountFacetsWithSearchAndNoSelectedFacetsAndConsents() {
-        Filter filter = new Filter(List.of(), "age", List.of("c1"));
+        Filter filter = new Filter(List.of(), "age", List.of("phs002715.c1", "phs000284.c1", "phs002385.c1"));
 
         MapSqlParameterSource params = new MapSqlParameterSource();
         String query = subject.createFacetSQLAndPopulateParams(filter, params);
@@ -147,7 +147,7 @@ void shouldCountFacetsWithSearchAndOneSelectedFacetsAndNoConsents() {
     void shouldCountFacetsWithSearchAndOneSelectedFacetsAndConsents() {
         Filter filter = new Filter(
             List.of(new Facet("phs002715", "study_ids_dataset_ids")),
-            "age", List.of("c1")
+            "age", List.of("phs002715.c1", "phs000284.c1", "phs002385.c1")
         );
 
         MapSqlParameterSource params = new MapSqlParameterSource();
@@ -191,7 +191,7 @@ void shouldCountFacetsNoSearchAndOneSelectedFacetsAndNoConsents() {
     void shouldCountFacetsNoSearchAndOneSelectedFacetsAndConsents() {
         Filter filter = new Filter(
             List.of(new Facet("phs002715", "study_ids_dataset_ids")),
-            "", List.of("c2")
+            "", List.of("phs000007.c2")
         );
 
         MapSqlParameterSource params = new MapSqlParameterSource();
@@ -235,7 +235,7 @@ void shouldCountFacetsWithSearchAndTwoSelectedFacetsInDifferentCatsAndConsents()
                 new Facet("phs000007", "study_ids_dataset_ids"),
                 new Facet("LOINC", "nsrr_harmonized")
             ),
-            "cola", List.of("c1")
+            "cola", List.of("LOINC.c1", "PhenX.c1", "phs000007.c1")
         );
 
         MapSqlParameterSource params = new MapSqlParameterSource();
@@ -281,7 +281,7 @@ void shouldCountFacetsNoSearchAndTwoSelectedFacetsInDifferentCatsAndConsents() {
                 new Facet("phs000007", "study_ids_dataset_ids"),
                 new Facet("LOINC", "nsrr_harmonized")
             ),
-            "", List.of("c1")
+            "", List.of("LOINC.c1", "PhenX.c1", "phs000007.c1")
         );
 
         MapSqlParameterSource params = new MapSqlParameterSource();

diff --git a/...est/java/edu/harvard/dbmi/avillach/dictionary/filter/ConceptFilterQueryGeneratorTest.java b/...est/java/edu/harvard/dbmi/avillach/dictionary/filter/ConceptFilterQueryGeneratorTest.java
@@ -68,7 +68,10 @@ void shouldGenerateForFHSFacet() {
 
     @Test
     void shouldGenerateForFHSFacetWithConsent1() {
-        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of("c1"));
+        Filter f = new Filter(List.of(new Facet(
+            "phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)),
+            "", List.of("phs000007.c1")
+        );
         QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged());
 
         List<Integer> actual = template.queryForList(pair.query(), pair.params(), Integer.class);
@@ -79,7 +82,7 @@ void shouldGenerateForFHSFacetWithConsent1() {
 
     @Test
     void shouldGenerateForFHSFacetWithConsent1And2() {
-        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of("c1", "c2"));
+        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of("phs000007.c1", "phs000007.c2"));
         QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged());
 
         List<Integer> actual = template.queryForList(pair.query(), pair.params(), Integer.class);
@@ -90,7 +93,7 @@ void shouldGenerateForFHSFacetWithConsent1And2() {
 
     @Test
     void shouldGenerateForFHSFacetWithConsent3() {
-        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of("c3"));
+        Filter f = new Filter(List.of(new Facet("phs000007", "FHS", "", "", null, null, "study_ids_dataset_ids", null)), "", List.of("dne.c3"));
         QueryParamPair pair = subject.generateFilterQuery(f, Pageable.unpaged());
 
         List<Integer> actual = template.queryForList(pair.query(), pair.params(), Integer.class);