a

hms-dbmi · Jul 18, 2024 · 5bab91c · 5bab91c
1 parent 1238ed0
commit 5bab91c
Show file tree

Hide file tree

Showing 4 changed files with 170 additions and 2 deletions.
diff --git a/no_facets.sql b/no_facets.sql
@@ -0,0 +1,18 @@
+SELECT
+    facet.facet_id, count(*) as facet_count
+FROM
+    facet
+    JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+    JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+    JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id
+    LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min'
+    LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max'
+    LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values'
+WHERE
+    continuous_min.value <> '' OR
+    continuous_max.value <> '' OR
+    categorical_values.value <> ''
+GROUP BY
+    facet.facet_id
+ORDER BY
+    facet_count DESC
diff --git a/one_facet.sql b/one_facet.sql
@@ -0,0 +1,60 @@
+(
+    SELECT
+        facet.facet_id, count(*) as facet_count
+    FROM
+        facet
+        JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+        JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+        JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id
+        LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min'
+        LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max'
+        LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values'
+    WHERE
+        fc.name = 'study_ids_dataset_ids'
+        AND (
+            continuous_min.value <> '' OR
+            continuous_max.value <> '' OR
+            categorical_values.value <> ''
+        )
+    GROUP BY
+        facet.facet_id
+    ORDER BY
+        facet_count DESC
+)
+UNION
+(
+    WITH matching_concepts AS (
+        SELECT
+            concept_node.concept_node_id AS concept_node_id
+        FROM
+            facet
+            JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+            JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+            JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id
+            LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min'
+            LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max'
+            LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values'
+        WHERE
+            fc.name = 'study_ids_dataset_ids'
+            AND facet.name IN ('phs000007')
+            AND (
+                continuous_min.value <> '' OR
+                continuous_max.value <> '' OR
+                categorical_values.value <> ''
+            )
+    )
+    SELECT
+        facet.facet_id, count(*) as facet_count
+    FROM
+        facet
+        JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+        JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+        JOIN matching_concepts ON fcn.concept_node_id = matching_concepts.concept_node_id
+    WHERE
+        fc.name <> 'study_ids_dataset_ids'
+    GROUP BY
+        facet.facet_id
+    ORDER BY
+        facet_count DESC
+)
+
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
@@ -16,6 +16,8 @@ class FacetQueryGeneratorTest {
     @Autowired
     FacetQueryGenerator generator;
 
+//    {"facets":[{"name":"LOINC","display":"LOINC","description":null,"count":1,"children":null,"category":"nsrr_harmonized","meta":null,"categoryRef":{"display":"Common Data Element Collection","name":"nsrr_harmonized","description":""}},{"name":"phs000007","display":"FHS","description":null,"count":1,"children":null,"category":"study_ids_dataset_ids","meta":null,"categoryRef":{"display":"Study IDs/Dataset IDs","name":"study_ids_dataset_ids","description":""}}],"search":""}
+
     @Test
     void shouldaaa() {
         Filter jim = new Filter(List.of(
@@ -26,8 +28,9 @@ void shouldaaa() {
         System.out.println(query);
     }
 
+
     @Test
-    void shouldaaa2() {
+    void shouldaa() {
         Filter jim = new Filter(List.of(
             new Facet("phs000007", "", "", null, null, "study_ids_dataset_ids", null)
         ), "");
@@ -36,7 +39,7 @@ void shouldaaa2() {
     }
 
     @Test
-    void shoudlbrungus() {
+    void shoulda() {
         Filter jim = new Filter(List.of(), "");
         String query = generator.createFacetSQLAndPopulateParams(jim, new MapSqlParameterSource());
         System.out.println(query);

diff --git a/two_cats.sql b/two_cats.sql
@@ -0,0 +1,87 @@
+WITH facet_category_cat_0_concepts AS (
+    SELECT
+        concept_node.concept_node_id
+    FROM
+        facet
+        JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+        JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+        JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id
+        LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min'
+        LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max'
+        LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values'
+    WHERE
+        (fc.name, facet.name) IN (('nsrr_harmonized', 'LOINC'))
+        AND (
+            continuous_min.value <> '' OR
+            continuous_max.value <> '' OR
+            categorical_values.value <> ''
+        )
+)
+,
+facet_category_cat_1_concepts AS (
+    SELECT
+        concept_node.concept_node_id
+    FROM
+        facet
+        JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+        JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+        JOIN concept_node ON concept_node.concept_node_id = fcn.concept_node_id
+        LEFT JOIN concept_node_meta AS continuous_min ON concept_node.concept_node_id = continuous_min.concept_node_id AND continuous_min.KEY = 'min'
+        LEFT JOIN concept_node_meta AS continuous_max ON concept_node.concept_node_id = continuous_max.concept_node_id AND continuous_max.KEY = 'max'
+        LEFT JOIN concept_node_meta AS categorical_values ON concept_node.concept_node_id = categorical_values.concept_node_id AND categorical_values.KEY = 'values'
+    WHERE
+        (fc.name, facet.name) IN (('study_ids_dataset_ids', 'phs000007'))
+        AND (
+            continuous_min.value <> '' OR
+            continuous_max.value <> '' OR
+            categorical_values.value <> ''
+        )
+)
+(
+    SELECT
+        facet.facet_id, count(*) as facet_count
+    FROM
+        facet
+        JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+        JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+    WHERE
+        fcn.concept_node_id IN (SELECT * FROM facet_category_cat_1_concepts)
+        AND fc.name = 'study_ids_dataset_ids'
+    GROUP BY
+        facet.facet_id
+    ORDER BY
+        facet_count DESC
+)
+
+    UNION
+(
+    SELECT
+        facet.facet_id, count(*) as facet_count
+    FROM
+        facet
+        JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+        JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+    WHERE
+        fcn.concept_node_id IN (SELECT * FROM facet_category_cat_0_concepts)
+        AND fc.name = 'nsrr_harmonized'
+    GROUP BY
+        facet.facet_id
+    ORDER BY
+        facet_count DESC
+)
+UNION
+(
+    SELECT
+        facet.facet_id, count(*) as facet_count
+    FROM
+        facet
+        JOIN facet_category fc on fc.facet_category_id = facet.facet_category_id
+        JOIN facet__concept_node fcn ON fcn.facet_id = facet.facet_id
+    WHERE
+        fc.name NOT IN ('nsrr_harmonized', 'study_ids_dataset_ids')
+        AND fcn.concept_node_id IN (SELECT * FROM facet_category_cat_0_concepts UNION SELECT * FROM facet_category_cat_1_concepts)
+    GROUP BY
+        facet.facet_id
+    ORDER BY
+        facet_count DESC
+)