Merge branch 'release' into ALS-7809

# Conflicts:
#	dictonaryReqeust.http

dictonaryReqeust.http

@@ -12,7 +12,8 @@ Content-Type: application/json
 POST http://localhost:80/search
 Content-Type: application/json
 
-{"@type":"GeneralQueryRequest","resourceCredentials":{},"query":{"searchTerm":"breast","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":10000000},"resourceUUID":null}
+{"@type":"GeneralQueryRequest","resourceCredentials":{},"query":{"searchTerm":"throat sore acute #8","includedTags":[],
+  "excludedTags":[],"returnTags":"true","offset":0,"limit":100000},"resourceUUID":null}
 
 ###
 

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/ConceptFilterQueryGenerator.java

@@ -82,37 +82,7 @@ public QueryParamPair generateFilterQuery(Filter filter, Pageable pageable) {
             params.addValue("consents", filter.consents());
         }
         clauses.add(createValuelessNodeFilter(filter.search(), filter.consents()));
-
-
-        String query = "(\n" + String.join("\n\tINTERSECT\n", clauses) + "\n)";
-        String superQuery = """
-            WITH q AS (
-                %s
-            )
-            %s
-            SELECT q.concept_node_id AS concept_node_id, max((1 + rank) * coalesce(rank_adjustment, 1)) AS rank
-            FROM q
-            LEFT JOIN allow_filtering ON allow_filtering.concept_node_id = q.concept_node_id
-            GROUP BY q.concept_node_id
-            ORDER BY max((1 + rank) * coalesce(rank_adjustment, 1)) DESC, q.concept_node_id ASC
-            """.formatted(query, RANK_ADJUSTMENTS);
-        // explanation of ORDER BY max((1 + rank) * coalesce(rank_adjustment, 1)) DESC
-        // you want to sort the best matches first, BUT anything that is marked as unfilterable should be put last
-        // coalesce will return the first non null value; this solves rows that aren't marked as filterable or not
-        // I then multiply that by 1 + rank instead of just rank so that a rank value of 0 for an unfilterable var
-        // is placed below a rank value of 0 for a filterable var
-        // Finally, I add the concept node id to the sort to keep it stable for ties, otherwise pagination gets weird
-
-        if (pageable.isPaged()) {
-            superQuery = superQuery + """
-                LIMIT :limit
-                OFFSET :offset
-                """;
-            params.addValue("limit", pageable.getPageSize()).addValue("offset", pageable.getOffset());
-        }
-
-        superQuery = " concepts_filtered_sorted AS (\n" + superQuery + "\n)";
-
+        String superQuery = getSuperQuery(pageable, clauses, params);
 
         return new QueryParamPair(superQuery, params);
     }
@@ -184,4 +154,78 @@ facet.name IN (:facets_for_category_%s ) AND facet_category.name = :category_%s
         }).toList();
     }
 
+    public QueryParamPair generateLegacyFilterQuery(Filter filter, Pageable pageable) {
+        MapSqlParameterSource params = new MapSqlParameterSource();
+        params.addValue("disallowed_meta_keys", disallowedMetaFields);
+        List<String> clauses = new java.util.ArrayList<>(List.of());
+        if (StringUtils.hasLength(filter.search())) {
+            params.addValue("dynamic_tsquery", filter.search().trim());
+        }
+        clauses.add(createDynamicValuelessNodeFilter(filter.search()));
+        String superQuery = getSuperQuery(pageable, clauses, params);
+
+        return new QueryParamPair(superQuery, params);
+    }
+
+    private String createDynamicValuelessNodeFilter(String search) {
+        String rankQuery = "0 as rank";
+        String rankWhere = "";
+        if (StringUtils.hasLength(search)) {
+            rankQuery = "ts_rank(searchable_fields, to_tsquery(:dynamic_tsquery)) AS rank";
+            rankWhere = "concept_node.searchable_fields @@ to_tsquery(:dynamic_tsquery) AND";
+        }
+        return """
+            SELECT
+                concept_node.concept_node_id,
+                %s
+            FROM
+                concept_node
+                LEFT JOIN dataset ON concept_node.dataset_id = dataset.dataset_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
+                %s
+                %s
+                (
+                    continuous_min.value <> '' OR
+                    continuous_max.value <> '' OR
+                    categorical_values.value <> ''
+                )
+            """
+            .formatted(rankQuery, rankWhere, "");
+    }
+
+    private static String getSuperQuery(Pageable pageable, List<String> clauses, MapSqlParameterSource params) {
+        String query = "(\n" + String.join("\n\tINTERSECT\n", clauses) + "\n)";
+        String superQuery = """
+            WITH q AS (
+                %s
+            )
+            %s
+            SELECT q.concept_node_id AS concept_node_id, max((1 + rank) * coalesce(rank_adjustment, 1)) AS rank
+            FROM q
+            LEFT JOIN allow_filtering ON allow_filtering.concept_node_id = q.concept_node_id
+            GROUP BY q.concept_node_id
+            ORDER BY max((1 + rank) * coalesce(rank_adjustment, 1)) DESC, q.concept_node_id ASC
+            """.formatted(query, RANK_ADJUSTMENTS);
+        // explanation of ORDER BY max((1 + rank) * coalesce(rank_adjustment, 1)) DESC
+        // you want to sort the best matches first, BUT anything that is marked as unfilterable should be put last
+        // coalesce will return the first non null value; this solves rows that aren't marked as filterable or not
+        // I then multiply that by 1 + rank instead of just rank so that a rank value of 0 for an unfilterable var
+        // is placed below a rank value of 0 for a filterable var
+        // Finally, I add the concept node id to the sort to keep it stable for ties, otherwise pagination gets weird
+
+        if (pageable.isPaged()) {
+            superQuery = superQuery + """
+                LIMIT :limit
+                OFFSET :offset
+                """;
+            params.addValue("limit", pageable.getPageSize()).addValue("offset", pageable.getOffset());
+        }
+
+        superQuery = " concepts_filtered_sorted AS (\n" + superQuery + "\n)";
+        return superQuery;
+    }
+
 }

src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchQueryMapper.java

@@ -3,32 +3,59 @@
 import com.fasterxml.jackson.databind.JsonNode;
 import com.fasterxml.jackson.databind.ObjectMapper;
 import edu.harvard.dbmi.avillach.dictionary.filter.Filter;
-import edu.harvard.dbmi.avillach.dictionary.filter.FilterProcessor;
 import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.LegacySearchQuery;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 import org.springframework.data.domain.PageRequest;
 import org.springframework.stereotype.Component;
 
 import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Arrays;
 import java.util.List;
+import java.util.stream.Collectors;
 
 @Component
 public class LegacySearchQueryMapper {
 
     private static final ObjectMapper objectMapper = new ObjectMapper();
-    private final FilterProcessor filterProcessor;
+    private static final Logger log = LoggerFactory.getLogger(LegacySearchQueryMapper.class);
 
-    public LegacySearchQueryMapper(FilterProcessor filterProcessor) {
-        this.filterProcessor = filterProcessor;
-    }
+    public LegacySearchQueryMapper() {}
 
     public LegacySearchQuery mapFromJson(String jsonString) throws IOException {
         JsonNode rootNode = objectMapper.readTree(jsonString);
         JsonNode queryNode = rootNode.get("query");
 
         String searchTerm = queryNode.get("searchTerm").asText();
         int limit = queryNode.get("limit").asInt();
-        Filter filter = filterProcessor.processsFilter(new Filter(List.of(), searchTerm, List.of()));
-        return new LegacySearchQuery(filter, PageRequest.of(0, limit));
+        searchTerm = constructTsQuery(searchTerm);
+        log.debug("Constructed Search Term: {}", searchTerm);
+        return new LegacySearchQuery(new Filter(List.of(), searchTerm, List.of()), PageRequest.of(0, limit));
+    }
+
+    // An attempt to provide OR search that will produce similar results to legacy search-prototype
+    private String constructTsQuery(String searchTerm) {
+        // Split on the | to enable or queries
+        String[] orGroups = searchTerm.split("\\|");
+        List<String> orClauses = new ArrayList<>();
+
+        for (String group : orGroups) {
+            // To replicate legacy search we will split using its regex [\\s\\p{Punct}]+
+            String[] tokens = group.trim().split("[\\s\\p{Punct}]+");
+
+            // Now we will combine the tokens in this group and '&' them together.
+            String andClause = Arrays.stream(tokens).filter(token -> !token.isBlank()) // remove empty tokens.
+                .map(token -> token + ":*") // add the wild card for search
+                .collect(Collectors.joining(" & "));
+
+            if (!andClause.isBlank()) {
+                orClauses.add(andClause);
+            }
+        }
+
+
+        return String.join(" | ", orClauses);
     }
 
 }

src/main/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchRepository.java

@@ -35,7 +35,7 @@ public LegacySearchRepository(
     }
 
     public List<SearchResult> getLegacySearchResults(Filter filter, Pageable pageable) {
-        QueryParamPair filterQ = filterGen.generateFilterQuery(filter, pageable);
+        QueryParamPair filterQ = filterGen.generateLegacyFilterQuery(filter, pageable);
         String sql = ALLOW_FILTERING_Q + ", " + filterQ.query() + """
                 SELECT concept_node.concept_path  AS conceptPath,
                    concept_node.display           AS display,

src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchControllerIntegrationTest.java

@@ -54,4 +54,38 @@ void shouldGetLegacyResponseByStudyID() throws IOException {
         searchResults.forEach(searchResult -> Assertions.assertEquals("phs000007", searchResult.result().studyId()));
     }
 
+    @Test
+    void shouldHandleORRequest() throws IOException {
+        String jsonString = """
+            {"query":{"searchTerm":"age","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}}
+            """;
+
+        ResponseEntity<LegacyResponse> legacyResponseResponseEntity = legacySearchController.legacySearch(jsonString);
+        Assertions.assertEquals(HttpStatus.OK, legacyResponseResponseEntity.getStatusCode());
+        LegacyResponse legacyResponseBody = legacyResponseResponseEntity.getBody();
+        Assertions.assertNotNull(legacyResponseBody);
+        Results results = legacyResponseBody.results();
+        List<SearchResult> ageSearchResults = results.searchResults();
+        Assertions.assertEquals(4, ageSearchResults.size());
+
+        jsonString = """
+            {"query":{"searchTerm":"physical|age","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}}
+            """;
+
+        legacyResponseResponseEntity = legacySearchController.legacySearch(jsonString);
+        Assertions.assertEquals(HttpStatus.OK, legacyResponseResponseEntity.getStatusCode());
+        legacyResponseBody = legacyResponseResponseEntity.getBody();
+        Assertions.assertNotNull(legacyResponseBody);
+        results = legacyResponseBody.results();
+        List<SearchResult> physicalORAgeSearchResults = results.searchResults();
+        Assertions.assertEquals(5, physicalORAgeSearchResults.size());
+
+        // Verify that age|physical has expanded the search results
+        Assertions.assertNotEquals(ageSearchResults.size(), physicalORAgeSearchResults.size());
+
+        // Verify the OR statement has more results
+        Assertions.assertTrue(ageSearchResults.size() < physicalORAgeSearchResults.size());
+    }
+
+
 }

src/test/java/edu/harvard/dbmi/avillach/dictionary/legacysearch/LegacySearchQueryMapperTest.java

@@ -28,12 +28,12 @@ void shouldParseSearchRequest() throws IOException {
         Filter filter = legacySearchQuery.filter();
         Pageable pageable = legacySearchQuery.pageable();
 
-        Assertions.assertEquals("age", filter.search());
+        Assertions.assertEquals("age:*", filter.search());
         Assertions.assertEquals(100, pageable.getPageSize());
     }
 
     @Test
-    void shouldReplaceUnderscore() throws IOException {
+    void shouldHandlePunct() throws IOException {
         String jsonString =
             """
                 {"query":{"searchTerm":"tutorial-biolincc_digitalis","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}}
@@ -43,7 +43,35 @@ void shouldReplaceUnderscore() throws IOException {
         Filter filter = legacySearchQuery.filter();
         Pageable pageable = legacySearchQuery.pageable();
 
-        Assertions.assertEquals("tutorial-biolincc/digitalis", filter.search());
+        Assertions.assertEquals("tutorial:* & biolincc:* & digitalis:*", filter.search());
+        Assertions.assertEquals(100, pageable.getPageSize());
+    }
+
+    @Test
+    void shouldHandleOR() throws IOException {
+        String jsonString = """
+            {"query":{"searchTerm":"sex|gender","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}}
+            """;
+
+        LegacySearchQuery legacySearchQuery = legacySearchQueryMapper.mapFromJson(jsonString);
+        Filter filter = legacySearchQuery.filter();
+        Pageable pageable = legacySearchQuery.pageable();
+
+        Assertions.assertEquals("sex:* | gender:*", filter.search());
+        Assertions.assertEquals(100, pageable.getPageSize());
+    }
+
+    @Test
+    void shouldHandleORAndPunct() throws IOException {
+        String jsonString = """
+            {"query":{"searchTerm":"sex|gender age","includedTags":[],"excludedTags":[],"returnTags":"true","offset":0,"limit":100}}
+            """;
+
+        LegacySearchQuery legacySearchQuery = legacySearchQueryMapper.mapFromJson(jsonString);
+        Filter filter = legacySearchQuery.filter();
+        Pageable pageable = legacySearchQuery.pageable();
+
+        Assertions.assertEquals("sex:* | gender:* & age:*", filter.search());
         Assertions.assertEquals(100, pageable.getPageSize());
     }