remove inordinately verbose debug logging

VEuPathDB · Oct 1, 2024 · 95d1413 · 95d1413
1 parent 27fb4a2
commit 95d1413
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Showing 3 changed files with 29 additions and 39 deletions.
diff --git a/build.gradle.kts b/build.gradle.kts
@@ -7,7 +7,7 @@
 
 // Project settings
 group   = "org.veupathdb.eda"
-version = "5.0.0"
+version = "5.0.1"
 
 plugins {
   `java-library`
@@ -25,10 +25,6 @@ tasks.withType<Jar> {
   duplicatesStrategy = DuplicatesStrategy.INCLUDE
 }
 
-//tasks.named("jar") {
-//  duplicatesStrategy =
-//}
-
 val test by tasks.getting(Test::class) {
   // use junit platform for unit tests
   useJUnitPlatform {

diff --git a/src/main/java/org/veupathdb/service/eda/subset/model/db/FilteredResultFactory.java b/src/main/java/org/veupathdb/service/eda/subset/model/db/FilteredResultFactory.java
@@ -189,7 +189,6 @@ private static CloseableIterator<Map<String, String>> oracleTabularSubsetIterato
     TreeNode<Entity> prunedEntityTree = pruneTree(study.getEntityTree(), filters, outputEntity);
 
     String sql = generateTabularSqlForTallRows(appDbSchema, outputVariables, outputEntity, filters, prunedEntityTree);
-    LOG.debug("Generated the following tabular SQL: {} with schema {}.", sql, appDbSchema);
 
     // gather the output columns; these will be used for the standard header and to look up DB column values
     List<String> outputColumns = getTabularOutputColumns(outputEntity, outputVariables);
@@ -225,7 +224,6 @@ public static void produceTabularSubset(DataSource dataSource, String appDbSchem
     String sql = reportConfig.requiresSorting()
         ? generateTabularSqlForWideRows(appDbSchema, outputVariables, outputEntity, filters, reportConfig, prunedEntityTree)
         : generateTabularSqlForTallRows(appDbSchema, outputVariables, outputEntity, filters, prunedEntityTree);
-    LOG.debug("Generated the following tabular SQL: " + sql);
 
     // gather the output columns; these will be used for the standard header and to look up DB column values
     List<String> outputColumns = getColumns(outputEntity, outputVariables, Entity::getPKColName, Variable::getId);;
@@ -464,7 +462,6 @@ public static Stream<TwoTuple<String, Long>> produceVariableDistribution(
       DataSource datasource, String appDbSchema, TreeNode<Entity> prunedEntityTree, Entity outputEntity,
       VariableWithValues distributionVariable, List<Filter> filters) {
     String sql = generateDistributionSql(appDbSchema, outputEntity, distributionVariable, filters, prunedEntityTree);
-    LOG.info("Generated the following distribution SQL: " + NL + sql + NL);
     return ResultSets.openStream(datasource, sql, "Produce variable distribution", row -> Optional.of(
         new TwoTuple<>(distributionVariable.getType().convertRowValueToStringValue(row), row.getLong(COUNT_COLUMN_NAME))));
   }
@@ -530,8 +527,6 @@ static List<String> getEntityIdsInFilters(List<Filter> filters) {
    */
   static String generateTabularSqlForTallRows(String appDbSchema, List<VariableWithValues> outputVariables, Entity outputEntity, List<Filter> filters, TreeNode<Entity> prunedEntityTree) {
 
-    LOG.debug("--------------------- generateTabularSql ------------------");
-
     String tallTblAbbrev = "tall";
     String ancestorTblAbbrev = "subset";
     return
@@ -579,8 +574,6 @@ static String generateTabularSqlForTallRows(String appDbSchema, List<VariableWit
    */
   static String generateTabularSqlForWideRows(String appDbSchema, List<VariableWithValues> outputVariables, Entity outputEntity, List<Filter> filters,
                                               TabularReportConfig reportConfig, TreeNode<Entity> prunedEntityTree) {
-    LOG.debug("--------------------- generateTabularSql paging sorting ------------------");
-
     String wideTabularWithClauseName = "wide_tabular";
     String subsetWithClauseName = "subset";
     String rowColName = "r";

diff --git a/src/main/java/org/veupathdb/service/eda/subset/model/reducer/MetadataFileBinaryProvider.java b/src/main/java/org/veupathdb/service/eda/subset/model/reducer/MetadataFileBinaryProvider.java
@@ -9,39 +9,40 @@
 import java.util.Optional;
 
 /**
- * Implementation of {@link BinaryMetadataProvider} that reads metadata from a meta.json file. This is designed to be
- * used by a consumer of the generated binary files.
+ * Implementation of {@link BinaryMetadataProvider} that reads metadata from a
+ * <code>meta.json</code> file. This is designed to be used by a consumer of the
+ * generated binary files.
  */
 public class MetadataFileBinaryProvider implements BinaryMetadataProvider {
 
-    private static final Logger LOG = LogManager.getLogger(MetadataFileBinaryProvider.class);
+  private static final Logger LOG = LogManager.getLogger(MetadataFileBinaryProvider.class);
 
-    private BinaryFilesManager binaryFilesManager;
+  private final BinaryFilesManager binaryFilesManager;
 
-    public MetadataFileBinaryProvider(BinaryFilesManager binaryFilesManager) {
-        this.binaryFilesManager = binaryFilesManager;
+  public MetadataFileBinaryProvider(BinaryFilesManager binaryFilesManager) {
+    this.binaryFilesManager = binaryFilesManager;
+  }
+
+  @Override
+  public Optional<BinaryProperties> getBinaryProperties(String studyAbbrev, Entity entity, String variableId) {
+    if (!binaryFilesManager.studyHasFiles(studyAbbrev)) {
+      LOG.error("Could not find files for study '{}' (using entity '{}' and variable '{}') while trying to find binary properties for a variable.", studyAbbrev, entity.getId(), variableId);
+      return Optional.empty();
+    }
+
+    Optional<BinaryFilesManager.Metadata> metadata = binaryFilesManager.readMetadata(studyAbbrev, entity);
+    if (metadata.isEmpty()) {
+      LOG.error("Unable to read metadata file for study '{}' (using entity '{}') even though files are present.", studyAbbrev, entity.getId());
+      return Optional.empty();
     }
 
-    @Override
-    public Optional<BinaryProperties> getBinaryProperties(String studyAbbrev, Entity entity, String variableId) {
-        if (!binaryFilesManager.studyHasFiles(studyAbbrev)) {
-            LOG.error("Could not find files for study '" + studyAbbrev + "' (using entity '" + entity.getId() + "' and variable '" + variableId + "') while trying to find binary properties for a variable.");
-            return Optional.empty();
-        }
-        Optional<BinaryFilesManager.Metadata> metadata = binaryFilesManager.readMetadata(studyAbbrev, entity);
-        if (metadata.isEmpty()) {
-            LOG.error("Unable to read metadata file for study '" + studyAbbrev + "' (using entity '" + entity.getId() + "') even though files are present.");
-            return Optional.empty();
-        }
-        Optional<BinaryFilesManager.VariableMeta> varMetadata = metadata.flatMap(meta -> meta.getVariableMetadata().stream()
-            .filter(varMeta -> varMeta.getVariableId().equals(variableId))
-            .findFirst());
-        if (varMetadata.isEmpty()) {
-            LOG.error("Unable to find metadata object for study '" + studyAbbrev + "', entity '" + entity.getId() + "', and variable '" + variableId + "' in metadata file.");
-            return Optional.empty();
-        }
-        BinaryProperties binaryProperties = varMetadata.get().getProperties();
-        LOG.info("Returning binary properties for  study '" + studyAbbrev + "', entity '" + entity.getId() + "', and variable '" + variableId + "': " + binaryProperties);
-        return Optional.of(binaryProperties);
+    Optional<BinaryFilesManager.VariableMeta> varMetadata = metadata.flatMap(meta -> meta.getVariableMetadata().stream()
+      .filter(varMeta -> varMeta.getVariableId().equals(variableId))
+      .findFirst());
+    if (varMetadata.isEmpty()) {
+      LOG.error("Unable to find metadata object for study '{}', entity '{}', and variable '{}' in metadata file.", studyAbbrev, entity.getId(), variableId);
     }
+
+    return varMetadata.map(BinaryFilesManager.VariableMeta::getProperties);
+  }
 }