[ALS-7760] Replicate Old Search in new Data-Dictionary (#53)

**[CHORE] GH Actions Fix**
- Fixed GitHub Actions to resolve workflow issues.

**Testing Enhancements**
- Added `@ActiveProfiles("test")` to testing classes to remove spam logs from `DataSourceVerifier` during unit tests.

**JSON Parsing Refactor**
- Created `JsonBlobParser` for improved JSON parsing.
- Refactored `ConceptResultSetUtil` to use `JsonBlobParser` for clearer separation of concerns.

**Code Cleanup**
- Removed unused imports from `ConceptShell` and `ContinuousConcept` classes to improve code readability.

**Legacy Search Feature**
- Implemented a new legacy search feature including service, controller, and related model classes.
- Updated `ConceptRepository` to support legacy search queries.
- Added test cases to ensure functionality.

**Testing Improvements**
- Added unit tests for `LegacySearchQueryMapper` to validate JSON parsing and string replacement.
- Introduced integration tests for `LegacySearchController` to verify search response correctness using a PostgreSQL container.

**Initial Configurations**
- Added application properties for database configuration and dashboard settings.
- Introduced Docker commands for local development with sample weights configuration.
- Included `weights.csv` and `dictonaryRequest.http` as sample data for testing API requests.

**Search Query Refactor**
- Created `LegacySearchRepository` to handle legacy search functionalities.
- Moved query logic (`ALLOW_FILTERING_Q`) to `QueryUtility`.
- Removed legacy search code from `ConceptRepository` for better separation of concerns.

**Filter Processing Refactor**
- Introduced `FilterProcessor` to centralize filter processing logic.
- Enhanced methods in `MetadataResultSetUtil` (`getDescription`, `getParentName`, `getParentDisplay`) for better validation using `StringUtils`.

**Repository Enhancements**
- Added `LegacySearchRepositoryTest` to verify legacy search functionalities.
- Refactored legacy search logic from `ConceptService` into `LegacySearchRepository`.
- Cleaned up unused imports and methods for better maintainability.

---

Co-authored-by: Luke Sikina <lucas.skina@gmail.com>

dictionaryweights/README.md

@@ -0,0 +1,11 @@
+## Docker commands for local development
+### Docker build
+```bash
+docker build --no-cache --build-arg SPRING_PROFILE=bdc-dev -t weights:latest .
+```
+
+### Docker run
+You will need a local weights.csv file.
+```bash
+    docker run --rm -t --name dictionary-weights --network=host -v ./weights.csv:/weights.csv weights:latest
+```

dictionaryweights/src/main/resources/application-bdc-dev.properties

@@ -0,0 +1,9 @@
+spring.application.name=dictionaryweights
+spring.main.web-application-type=none
+
+spring.datasource.url=jdbc:postgresql://localhost:5432/dictionary_db?currentSchema=dict
+spring.datasource.username=username
+spring.datasource.password=password
+spring.datasource.driver-class-name=org.postgresql.Driver
+
+weights.filename=/weights.csv

dictionaryweights/weights.csv

@@ -0,0 +1,7 @@
+concept_node.DISPLAY,2
+concept_node.CONCEPT_PATH,2
+dataset.FULL_NAME,1
+dataset.DESCRIPTION,1
+parent.DISPLAY,1
+grandparent.DISPLAY,1
+concept_node_meta_str,1

dictonaryReqeust.http

@@ -0,0 +1,15 @@
+# curl 'https://dev.picsure.biodatacatalyst.nhlbi.nih.gov/picsure/proxy/dictionary-api/concepts?page_number=1&page_size=1'
+#  -H 'origin: https://dev.picsure.biodatacatalyst.nhlbi.nih.gov'
+#  -H 'referer: https://dev.picsure.biodatacatalyst.nhlbi.nih.gov/'
+#  --data-raw '{"facets":[],"search":"","consents":[]}'
+POST http://localhost:80/concepts?page_number=0&page_size=100
+Content-Type: application/json
+
+{"facets":[],"search":"lipid triglyceride"}
+
+###
+
+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}

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

@@ -3,6 +3,7 @@
 import edu.harvard.dbmi.avillach.dictionary.concept.model.Concept;
 import edu.harvard.dbmi.avillach.dictionary.filter.Filter;
 import edu.harvard.dbmi.avillach.dictionary.filter.QueryParamPair;
+import edu.harvard.dbmi.avillach.dictionary.legacysearch.SearchResultRowMapper;
 import edu.harvard.dbmi.avillach.dictionary.util.MapExtractor;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
@@ -15,32 +16,19 @@
 import java.util.Map;
 import java.util.Optional;
 
+import static edu.harvard.dbmi.avillach.dictionary.util.QueryUtility.ALLOW_FILTERING_Q;
+
+
 @Repository
 public class ConceptRepository {
 
-    private static final String ALLOW_FILTERING_Q = """
-        WITH allow_filtering AS (
-            SELECT
-                concept_node.concept_node_id AS concept_node_id,
-                (string_agg(concept_node_meta.value, ' ') NOT LIKE '%' || 'true' || '%') AS allowFiltering
-            FROM
-                concept_node
-                JOIN concept_node_meta ON
-                    concept_node.concept_node_id = concept_node_meta.concept_node_id
-                    AND concept_node_meta.KEY IN (:disallowed_meta_keys)
-            GROUP BY
-                concept_node.concept_node_id
-        )
-        """;
-
     private final NamedParameterJdbcTemplate template;
     private final ConceptRowMapper mapper;
     private final ConceptFilterQueryGenerator filterGen;
     private final ConceptMetaExtractor conceptMetaExtractor;
     private final ConceptResultSetExtractor conceptResultSetExtractor;
     private final List<String> disallowedMetaFields;
 
-
     @Autowired
     public ConceptRepository(
         NamedParameterJdbcTemplate template, ConceptRowMapper mapper, ConceptFilterQueryGenerator filterGen,
@@ -240,4 +228,6 @@ WITH RECURSIVE nodes AS (
         return Optional.ofNullable(template.query(sql, params, conceptResultSetExtractor));
 
     }
+
+
 }

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

@@ -2,83 +2,43 @@
 
 import edu.harvard.dbmi.avillach.dictionary.concept.model.CategoricalConcept;
 import edu.harvard.dbmi.avillach.dictionary.concept.model.ContinuousConcept;
-import org.json.JSONArray;
-import org.json.JSONException;
+import edu.harvard.dbmi.avillach.dictionary.util.JsonBlobParser;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
-import java.math.BigDecimal;
-import java.math.BigInteger;
 import java.sql.ResultSet;
 import java.sql.SQLException;
-import java.util.ArrayList;
 import java.util.List;
-import java.util.stream.Collectors;
 
 @Component
 public class ConceptResultSetUtil {
 
     private static final Logger log = LoggerFactory.getLogger(ConceptResultSetUtil.class);
+    private final JsonBlobParser jsonBlobParser;
+
+    @Autowired
+    public ConceptResultSetUtil(JsonBlobParser jsonBlobParser) {
+        this.jsonBlobParser = jsonBlobParser;
+    }
 
     public CategoricalConcept mapCategorical(ResultSet rs) throws SQLException {
         return new CategoricalConcept(
             rs.getString("concept_path"), rs.getString("name"), rs.getString("display"), rs.getString("dataset"),
-            rs.getString("description"), rs.getString("values") == null ? List.of() : parseValues(rs.getString("values")),
+            rs.getString("description"), rs.getString("values") == null ? List.of() : jsonBlobParser.parseValues(rs.getString("values")),
             rs.getBoolean("allowFiltering"), rs.getString("studyAcronym"), null, null
         );
     }
 
     public ContinuousConcept mapContinuous(ResultSet rs) throws SQLException {
         return new ContinuousConcept(
             rs.getString("concept_path"), rs.getString("name"), rs.getString("display"), rs.getString("dataset"),
-            rs.getString("description"), rs.getBoolean("allowFiltering"), parseMin(rs.getString("values")),
-            parseMax(rs.getString("values")), rs.getString("studyAcronym"), null
+            rs.getString("description"), rs.getBoolean("allowFiltering"), jsonBlobParser.parseMin(rs.getString("values")),
+            jsonBlobParser.parseMax(rs.getString("values")), rs.getString("studyAcronym"), null
         );
     }
 
-    public List<String> parseValues(String valuesArr) {
-        try {
-            ArrayList<String> vals = new ArrayList<>();
-            JSONArray arr = new JSONArray(valuesArr);
-            for (int i = 0; i < arr.length(); i++) {
-                vals.add(arr.getString(i));
-            }
-            return vals;
-        } catch (JSONException ex) {
-            return List.of();
-        }
-    }
 
-    public Float parseMin(String valuesArr) {
-        return parseFromIndex(valuesArr, 0);
-    }
 
-    private Float parseFromIndex(String valuesArr, int index) {
-        try {
-            JSONArray arr = new JSONArray(valuesArr);
-            if (arr.length() != 2) {
-                return 0F;
-            }
-            Object raw = arr.get(index);
-            return switch (raw) {
-                case Double d -> d.floatValue();
-                case Integer i -> i.floatValue();
-                case String s -> Double.valueOf(s).floatValue();
-                case BigDecimal d -> d.floatValue();
-                case BigInteger i -> i.floatValue();
-                default -> 0f;
-            };
-        } catch (JSONException ex) {
-            log.warn("Invalid json array for values: ", ex);
-            return 0F;
-        } catch (NumberFormatException ex) {
-            log.warn("Valid json array but invalid val within: ", ex);
-            return 0F;
-        }
-    }
-
-    public Float parseMax(String valuesArr) {
-        return parseFromIndex(valuesArr, 1);
-    }
 }

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

@@ -70,4 +70,5 @@ public Optional<Concept> conceptTree(String dataset, String conceptPath, int dep
     public Optional<Concept> conceptDetailWithoutAncestors(String dataset, String conceptPath) {
         return getConcept(dataset, conceptPath, false);
     }
+
 }

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ConceptShell.java

@@ -1,7 +1,6 @@
 package edu.harvard.dbmi.avillach.dictionary.concept.model;
 
 import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset;
-import jakarta.annotation.Nullable;
 
 import java.util.List;
 import java.util.Map;

src/main/java/edu/harvard/dbmi/avillach/dictionary/concept/model/ContinuousConcept.java

@@ -4,7 +4,6 @@
 import edu.harvard.dbmi.avillach.dictionary.dataset.Dataset;
 import jakarta.annotation.Nullable;
 
-import java.util.ArrayList;
 import java.util.List;
 import java.util.Map;
 import java.util.Objects;

src/main/java/edu/harvard/dbmi/avillach/dictionary/datasource/DataSourceVerifier.java

@@ -3,15 +3,17 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Profile;
 import org.springframework.context.event.ContextRefreshedEvent;
 import org.springframework.context.event.EventListener;
-import org.springframework.stereotype.Service;
 
 import javax.sql.DataSource;
 import java.sql.Connection;
 import java.sql.SQLException;
 
-@Service
+@Profile("!test")
+@Configuration
 public class DataSourceVerifier {
 
     private static final Logger LOG = LoggerFactory.getLogger(DataSourceVerifier.class);
@@ -28,11 +30,10 @@ public void verifyDataSourceConnection() {
         try (Connection connection = dataSource.getConnection()) {
             if (connection != null) {
                 LOG.info("Datasource connection verified successfully.");
-            } else {
-                LOG.info("Failed to obtain a connection from the datasource.");
             }
         } catch (SQLException e) {
-            LOG.info("Error verifying datasource connection: {}", e.getMessage());
+            LOG.info("Failed to obtain a connection from the datasource.");
+            LOG.debug("Error verifying datasource connection: {}", e.getMessage());
         }
     }
 

src/main/java/edu/harvard/dbmi/avillach/dictionary/facet/FilterPreProcessor.java

@@ -1,22 +1,28 @@
 package edu.harvard.dbmi.avillach.dictionary.facet;
 
 import edu.harvard.dbmi.avillach.dictionary.filter.Filter;
+import edu.harvard.dbmi.avillach.dictionary.filter.FilterProcessor;
+import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.core.MethodParameter;
 import org.springframework.http.HttpInputMessage;
 import org.springframework.http.converter.HttpMessageConverter;
-import org.springframework.util.StringUtils;
 import org.springframework.web.bind.annotation.ControllerAdvice;
 import org.springframework.web.servlet.mvc.method.annotation.RequestBodyAdvice;
 
 import java.io.IOException;
 import java.lang.reflect.Type;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.function.Function;
 
 @ControllerAdvice
 public class FilterPreProcessor implements RequestBodyAdvice {
+
+    private final FilterProcessor filterProcessor;
+
+    @Autowired
+    public FilterPreProcessor(FilterProcessor filterProcessor) {
+        this.filterProcessor = filterProcessor;
+    }
+
+
     @Override
     public boolean supports(MethodParameter methodParameter, Type targetType, Class<? extends HttpMessageConverter<?>> converterType) {
         return true;
@@ -35,26 +41,13 @@ public Object afterBodyRead(
         Class<? extends HttpMessageConverter<?>> converterType
     ) {
         if (body instanceof Filter filter) {
-            List<Facet> newFacets = filter.facets();
-            List<String> newConsents = filter.consents();
-            if (filter.facets() != null) {
-                newFacets = new ArrayList<>(filter.facets());
-                newFacets.sort(Comparator.comparing(Facet::name));
-            }
-            if (filter.consents() != null) {
-                newConsents = new ArrayList<>(newConsents);
-                newConsents.sort(Comparator.comparing(Function.identity()));
-            }
-            filter = new Filter(newFacets, filter.search(), newConsents);
-
-            if (StringUtils.hasLength(filter.search())) {
-                filter = new Filter(filter.facets(), filter.search().replaceAll("_", "/"), filter.consents());
-            }
-            return filter;
+            return filterProcessor.processsFilter(filter);
         }
         return body;
     }
 
+
+
     @Override
     public Object handleEmptyBody(
         Object body, HttpInputMessage inputMessage, MethodParameter parameter, Type targetType,

src/main/java/edu/harvard/dbmi/avillach/dictionary/filter/FilterProcessor.java

@@ -0,0 +1,34 @@
+package edu.harvard.dbmi.avillach.dictionary.filter;
+
+import edu.harvard.dbmi.avillach.dictionary.facet.Facet;
+import org.springframework.stereotype.Component;
+import org.springframework.util.StringUtils;
+
+import java.util.ArrayList;
+import java.util.Comparator;
+import java.util.List;
+import java.util.function.Function;
+
+@Component
+public class FilterProcessor {
+
+    public Filter processsFilter(Filter filter) {
+        List<Facet> newFacets = filter.facets();
+        List<String> newConsents = filter.consents();
+        if (filter.facets() != null) {
+            newFacets = new ArrayList<>(filter.facets());
+            newFacets.sort(Comparator.comparing(Facet::name));
+        }
+        if (filter.consents() != null) {
+            newConsents = new ArrayList<>(newConsents);
+            newConsents.sort(Comparator.comparing(Function.identity()));
+        }
+        filter = new Filter(newFacets, filter.search(), newConsents);
+
+        if (StringUtils.hasLength(filter.search())) {
+            filter = new Filter(filter.facets(), filter.search().replaceAll("_", "/"), filter.consents());
+        }
+        return filter;
+    }
+
+}

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

@@ -0,0 +1,32 @@
+package edu.harvard.dbmi.avillach.dictionary.legacysearch;
+
+import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.LegacyResponse;
+import edu.harvard.dbmi.avillach.dictionary.legacysearch.model.LegacySearchQuery;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.http.ResponseEntity;
+import org.springframework.stereotype.Controller;
+import org.springframework.web.bind.annotation.RequestBody;
+import org.springframework.web.bind.annotation.RequestMapping;
+
+import java.io.IOException;
+
+@Controller
+public class LegacySearchController {
+
+    private final LegacySearchService legacySearchService;
+    private final LegacySearchQueryMapper legacySearchQueryMapper;
+
+    @Autowired
+    public LegacySearchController(LegacySearchService legacySearchService, LegacySearchQueryMapper legacySearchQueryMapper) {
+        this.legacySearchService = legacySearchService;
+        this.legacySearchQueryMapper = legacySearchQueryMapper;
+    }
+
+    @RequestMapping(path = "/search")
+    public ResponseEntity<LegacyResponse> legacySearch(@RequestBody String jsonString) throws IOException {
+        LegacySearchQuery legacySearchQuery = legacySearchQueryMapper.mapFromJson(jsonString);
+        return ResponseEntity
+            .ok(new LegacyResponse(legacySearchService.getSearchResults(legacySearchQuery.filter(), legacySearchQuery.pageable())));
+    }
+
+}