From 52ede264f605e2e9c82637c5d10667bef3527271 Mon Sep 17 00:00:00 2001
From: Luke Sikina <lucas.skina@gmail.com>
Date: Thu, 13 Mar 2025 16:03:41 -0400
Subject: [PATCH] [ALS-8396] When no meta exists, dont filter out var

---
 .../dictionary/concept/ConceptRepository.java | 19 +++++++++----------
 .../concept/ConceptRepositoryTest.java        |  6 ++++++
 2 files changed, 15 insertions(+), 10 deletions(-)

diff --git a/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java b/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java
index a25dc2f..551eb2a 100644
--- a/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java
+++ b/src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepository.java
@@ -4,6 +4,7 @@
 import edu.harvard.dbmi.avillach.dictionary.filter.Filter;
 import edu.harvard.dbmi.avillach.dictionary.filter.QueryParamPair;
 import edu.harvard.dbmi.avillach.dictionary.util.MapExtractor;
+import edu.harvard.dbmi.avillach.dictionary.util.QueryUtility;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.data.domain.Pageable;
@@ -15,8 +16,6 @@
 import java.util.Map;
 import java.util.Optional;
 
-import static edu.harvard.dbmi.avillach.dictionary.util.QueryUtility.ALLOW_FILTERING_Q;
-
 
 @Repository
 public class ConceptRepository {
@@ -47,7 +46,7 @@ public ConceptRepository(
 
     public List<Concept> getConcepts(Filter filter, Pageable pageable) {
         QueryParamPair filterQ = filterGen.generateFilterQuery(filter, pageable);
-        String sql = ALLOW_FILTERING_Q + ", " + filterQ.query()
+        String sql = QueryUtility.ALLOW_FILTERING_Q + ", " + filterQ.query()
             + """
                 SELECT
                     concept_node.*,
@@ -55,7 +54,7 @@ public List<Concept> getConcepts(Filter filter, Pageable pageable) {
                     ds.abbreviation AS studyAcronym,
                     continuous_min.VALUE as min, continuous_max.VALUE as max,
                     categorical_values.VALUE as values,
-                    allow_filtering.allowFiltering AS allowFiltering,
+                    coalesce(allow_filtering.allowFiltering, TRUE) AS allowFiltering,
                     meta_description.VALUE AS description
                 FROM
                     concept_node
@@ -82,7 +81,7 @@ public long countConcepts(Filter filter) {
     }
 
     public Optional<Concept> getConcept(String dataset, String conceptPath) {
-        String sql = ALLOW_FILTERING_Q
+        String sql = QueryUtility.ALLOW_FILTERING_Q
             + """
                 SELECT
                     concept_node.*,
@@ -90,7 +89,7 @@ public Optional<Concept> getConcept(String dataset, String conceptPath) {
                     ds.abbreviation AS studyAcronym,
                     continuous_min.VALUE as min, continuous_max.VALUE as max,
                     categorical_values.VALUE as values,
-                    allow_filtering.allowFiltering AS allowFiltering,
+                    coalesce(allow_filtering.allowFiltering, TRUE) AS allowFiltering,
                     meta_description.VALUE AS description
                 FROM
                     concept_node
@@ -146,7 +145,7 @@ public Map<Concept, Map<String, String>> getConceptMetaForConcepts(List<Concept>
     }
 
     public Optional<Concept> getConceptTree(String dataset, String conceptPath, int depth) {
-        String sql = ALLOW_FILTERING_Q
+        String sql = QueryUtility.ALLOW_FILTERING_Q
             + """
                     , core_query AS (
                         WITH RECURSIVE nodes AS (
@@ -207,7 +206,7 @@ WITH RECURSIVE nodes AS (
                         continuous_min.VALUE AS min, continuous_max.VALUE AS max,
                         categorical_values.VALUE AS values,
                         meta_description.VALUE AS description,
-                        allow_filtering.allowFiltering AS allowFiltering,
+                        coalesce(allow_filtering.allowFiltering, TRUE) AS allowFiltering,
                         core_query.depth AS depth
                     FROM
                         concept_node
@@ -232,7 +231,7 @@ WITH RECURSIVE nodes AS (
 
 
     public List<Concept> getConceptsByPathWithMetadata(List<String> conceptPaths) {
-        String sql = ALLOW_FILTERING_Q + ", "
+        String sql = QueryUtility.ALLOW_FILTERING_Q + ", "
             + """
                 filtered_concepts AS (
                      SELECT
@@ -261,7 +260,7 @@ concept_node_meta.concept_node_id IN (
                      ds.abbreviation AS studyAcronym,
                      continuous_min.VALUE as min, continuous_max.VALUE as max,
                      categorical_values.VALUE as values,
-                     allow_filtering.allowFiltering AS allowFiltering,
+                     coalesce(allow_filtering.allowFiltering, TRUE) AS allowFiltering,
                      meta_description.VALUE AS description,
                      aggregated_meta.metadata AS metadata
                  FROM
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
index 432ecfd..61d4722 100644
--- a/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java
+++ b/src/test/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptRepositoryTest.java
@@ -41,6 +41,12 @@ static void mySQLProperties(DynamicPropertyRegistry registry) {
         registry.add("spring.datasource.db", databaseContainer::getDatabaseName);
     }
 
+    @Test
+    void shouldMarkConceptThatHasNoStimatizedMetaAsAllowFiltering() {
+        Boolean actual = subject.getConcept("1", "\\Variant Data Type\\WGS\\").map(Concept::allowFiltering).get();
+        Assertions.assertTrue(actual);
+    }
+
     @Test
     void shouldListAllConcepts() {
         List<Concept> actual = subject.getConcepts(new Filter(List.of(), "", List.of()), Pageable.unpaged());