Updated variable factory to no longer check existence of files to support file dumper tool

Author: dmgaldi

build.gradle.kts

@@ -7,7 +7,7 @@
 
 // Project settings
 group   = "org.veupathdb.eda"
-version = "3.8.3"
+version = "4.0.0"
 
 plugins {
   `java-library`

src/main/java/org/veupathdb/service/eda/ss/model/db/VariableFactory.java

@@ -16,6 +16,7 @@
 import java.util.Map;
 import java.util.Optional;
 import java.util.concurrent.ConcurrentHashMap;
+import java.util.function.Function;
 
 import static org.gusdb.fgputil.FormatUtil.NL;
 import static org.veupathdb.service.eda.ss.model.db.DB.Tables.AttributeGraph.Columns.*;
@@ -26,23 +27,28 @@ public class VariableFactory {
   private final DataSource _dataSource;
   private final String _appDbSchema;
   private final Optional<BinaryMetadataProvider> _binaryMetadataProvider;
-  private final BinaryFilesManager _binaryFilesManager;
   private final Map<String,Boolean> _studyHasFilesMap;
+  private final Function<String, Boolean> _shouldAppendMetaForStudy;
 
-  public VariableFactory(DataSource dataSource, String appDbSchema, BinaryMetadataProvider binaryMetadataProvider, BinaryFilesManager binaryFilesManager) {
+  public VariableFactory(DataSource dataSource,
+                         String appDbSchema,
+                         BinaryMetadataProvider binaryMetadataProvider,
+                         Function<String, Boolean> shouldAppendMetaForStudy) {
     _dataSource = dataSource;
     _appDbSchema = appDbSchema;
     _binaryMetadataProvider = Optional.ofNullable(binaryMetadataProvider);
-    _binaryFilesManager = binaryFilesManager;
+    _shouldAppendMetaForStudy = shouldAppendMetaForStudy;
     _studyHasFilesMap = new ConcurrentHashMap<>();
   }
 
+
   List<Variable> loadVariables(String studyAbbrev, Entity entity) {
 
     String sql = generateStudyVariablesListSql(entity, _appDbSchema);
 
-    Optional<BinaryMetadataProvider> metadataProvider = _binaryMetadataProvider.flatMap(provider ->
-        _studyHasFilesMap.computeIfAbsent(studyAbbrev, _binaryFilesManager::studyHasFiles) ? Optional.of(provider) : Optional.empty());
+    Optional<BinaryMetadataProvider> metadataProvider = _shouldAppendMetaForStudy.apply(studyAbbrev)
+        ? _binaryMetadataProvider
+        : Optional.empty();
 
     return new SQLRunner(_dataSource, sql, "Get entity variables metadata for: '" + entity.getDisplayName() + "'").executeQuery(rs -> {
       List<Variable> variables = new ArrayList<>();

src/test/java/org/veupathdb/service/eda/ss/model/db/EntityResultSetUtilsTest.java

@@ -40,7 +40,7 @@ public void beforeEach() {
     Mockito.when(_binaryMetadataProvider.getBinaryProperties(Mockito.anyString(), Mockito.any(Entity.class), Mockito.anyString()))
             .thenReturn(Optional.empty());
     Study study = new StudyFactory(StubDb.getDataSource(), APP_DB_SCHEMA, USER_STUDIES_FLAG,
-        new VariableFactory(StubDb.getDataSource(), APP_DB_SCHEMA, _binaryMetadataProvider, _binaryFilesManager)).getStudyById(LoadStudyTest.STUDY_ID);
+        new VariableFactory(StubDb.getDataSource(), APP_DB_SCHEMA, _binaryMetadataProvider, studyId -> false)).getStudyById(LoadStudyTest.STUDY_ID);
     new MockFilters(study);
   }
 

src/test/java/org/veupathdb/service/eda/ss/model/db/LoadStudyTest.java

@@ -126,7 +126,7 @@ void testReadAllVariables() {
 
     Entity entity = entityIdMap.get("GEMS_Part");
 
-    List<Variable> variables = new VariableFactory(datasource, APP_DB_SCHEMA, binaryMetadataProvider, binaryFilesManager)
+    List<Variable> variables = new VariableFactory(datasource, APP_DB_SCHEMA, binaryMetadataProvider, studyId -> false)
         .loadVariables(STUDY_ID, entity);
 
     assertEquals(5, variables.size());
@@ -135,7 +135,7 @@ void testReadAllVariables() {
   @Test
   @DisplayName("Load study test") 
   void testLoadStudy() {
-    VariableFactory variableFactory = new VariableFactory(datasource, APP_DB_SCHEMA, binaryMetadataProvider, binaryFilesManager);
+    VariableFactory variableFactory = new VariableFactory(datasource, APP_DB_SCHEMA, binaryMetadataProvider, studyId -> false);
     Study study = new StudyFactory(datasource, APP_DB_SCHEMA, USER_STUDIES_FLAG, variableFactory).getStudyById(STUDY_ID);
     assertNotNull(study);
   }

src/test/java/org/veupathdb/service/eda/ss/model/db/StudySubsettingUtilsTest.java

@@ -55,7 +55,7 @@ public static void setUp() {
     _model = new MockModel();
     _filtesFromMockStudy = new MockFilters(_model.study);
     _dataSource = StubDb.getDataSource();
-    _variableFactory = new VariableFactory(_dataSource, APP_DB_SCHEMA, new EmptyBinaryMetadataProvider(), bfm);
+    _variableFactory = new VariableFactory(_dataSource, APP_DB_SCHEMA, new EmptyBinaryMetadataProvider(), studyId -> false);
     Study study = new StudyFactory(_dataSource, APP_DB_SCHEMA, USER_STUDIES_FLAG, _variableFactory).getStudyById(LoadStudyTest.STUDY_ID);
     _filtersFromDbStudy = new MockFilters(study);
   }

src/test/java/org/veupathdb/service/eda/ss/service/StudiesTest.java

@@ -37,7 +37,7 @@ public static void setUp() {
     _dataSource = StubDb.getDataSource();
     _binaryFilesManager = Mockito.mock(BinaryFilesManager.class);
     Mockito.when(_binaryFilesManager.studyHasFiles(Mockito.anyString())).thenReturn(false);
-    _variableFactory = new VariableFactory(_dataSource, APP_DB_SCHEMA, new EmptyBinaryMetadataProvider(), _binaryFilesManager);
+    _variableFactory = new VariableFactory(_dataSource, APP_DB_SCHEMA, new EmptyBinaryMetadataProvider(), studyId -> false);
     Study study = new StudyFactory(_dataSource, APP_DB_SCHEMA, USER_STUDIES_FLAG, _variableFactory).getStudyById("DS-2324");
     _filtersForTesting = new MockFilters(study);
   }