Replace wildcard imports with specifics for external libs (#1134)

DataBiosphere · Jan 17, 2025 · 2429a14 · 2429a14
1 parent 2367166
commit 2429a14
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Showing 16 changed files with 46 additions and 26 deletions.
diff --git a/service/src/main/java/bio/terra/tanagra/service/UnderlayService.java b/service/src/main/java/bio/terra/tanagra/service/UnderlayService.java
@@ -29,7 +29,7 @@
 import bio.terra.tanagra.underlay.entitymodel.*;
 import bio.terra.tanagra.underlay.serialization.*;
 import com.google.common.collect.ImmutableMap;
-import jakarta.annotation.*;
+import jakarta.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.Collections;
 import java.util.HashMap;

diff --git a/service/src/main/java/bio/terra/tanagra/service/artifact/model/CohortRevision.java b/service/src/main/java/bio/terra/tanagra/service/artifact/model/CohortRevision.java
@@ -9,7 +9,7 @@
 import java.util.Collections;
 import java.util.List;
 import java.util.Objects;
-import java.util.stream.*;
+import java.util.stream.Stream;
 
 @SuppressWarnings("PMD.ExcessivePublicCount")
 public final class CohortRevision {
@@ -238,7 +238,7 @@ public static class CriteriaGroupSection {
     @SuppressWarnings("checkstyle:ParameterNumber")
     private CriteriaGroupSection(
         String id,
-        String displayName,
+        @Nullable String displayName,
         List<CriteriaGroup> criteriaGroups,
         List<CriteriaGroup> secondConditionCriteriaGroups,
         BooleanAndOrFilter.LogicalOperator operator,
@@ -269,6 +269,7 @@ public String getId() {
       return id;
     }
 
+    @Nullable
     public String getDisplayName() {
       return displayName;
     }

diff --git a/service/src/main/java/bio/terra/tanagra/service/filter/FilterBuilderService.java b/service/src/main/java/bio/terra/tanagra/service/filter/FilterBuilderService.java
@@ -30,7 +30,8 @@
 import java.util.Map;
 import java.util.Objects;
 import java.util.Set;
-import java.util.stream.*;
+import java.util.stream.Collectors;
+import java.util.stream.Stream;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.tuple.Pair;
 import org.slf4j.Logger;

diff --git a/underlay/src/main/java/bio/terra/tanagra/api/filter/TemporalPrimaryFilter.java b/underlay/src/main/java/bio/terra/tanagra/api/filter/TemporalPrimaryFilter.java
@@ -7,7 +7,8 @@
 import bio.terra.tanagra.underlay.entitymodel.*;
 import com.google.common.collect.ImmutableList;
 import jakarta.annotation.Nullable;
-import java.util.*;
+import java.util.List;
+import java.util.Objects;
 
 public class TemporalPrimaryFilter extends EntityFilter {
   private final Underlay underlay;

diff --git a/underlay/src/main/java/bio/terra/tanagra/api/shared/ValueDisplay.java b/underlay/src/main/java/bio/terra/tanagra/api/shared/ValueDisplay.java
@@ -1,7 +1,8 @@
 package bio.terra.tanagra.api.shared;
 
-import com.google.common.collect.*;
-import java.util.*;
+import com.google.common.collect.ImmutableList;
+import java.util.List;
+import java.util.Objects;
 
 public class ValueDisplay {
   private final Literal value;

diff --git a/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BQExecutor.java b/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BQExecutor.java
@@ -16,7 +16,7 @@
 import com.google.cloud.bigquery.Table;
 import com.google.cloud.bigquery.TableId;
 import com.google.cloud.bigquery.TableResult;
-import com.google.cloud.storage.*;
+import com.google.cloud.storage.BlobId;
 import com.google.common.collect.Iterables;
 import java.math.BigInteger;
 import java.sql.Timestamp;

diff --git a/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BQExecutorInfrastructure.java b/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BQExecutorInfrastructure.java
@@ -1,8 +1,8 @@
 package bio.terra.tanagra.query.bigquery;
 
-import com.google.common.collect.*;
-import jakarta.annotation.*;
-import java.util.*;
+import com.google.common.collect.ImmutableList;
+import jakarta.annotation.Nullable;
+import java.util.List;
 
 public class BQExecutorInfrastructure {
   private final String queryProjectId;
@@ -12,7 +12,7 @@ public class BQExecutorInfrastructure {
 
   private BQExecutorInfrastructure(
       String queryProjectId,
-      String datasetLocation,
+      @Nullable String datasetLocation,
       List<String> exportDatasetIds,
       List<String> exportBucketNames) {
     this.queryProjectId = queryProjectId;
@@ -40,14 +40,17 @@ public String getQueryProjectId() {
     return queryProjectId;
   }
 
+  @Nullable
   public String getDatasetLocation() {
     return datasetLocation;
   }
 
+  @Nullable
   public ImmutableList<String> getExportDatasetIds() {
     return exportDatasetIds;
   }
 
+  @Nullable
   public ImmutableList<String> getExportBucketNames() {
     return exportBucketNames;
   }

diff --git a/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BQQueryRunner.java b/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BQQueryRunner.java
@@ -35,9 +35,15 @@
 import com.google.common.annotations.VisibleForTesting;
 import com.google.common.collect.HashBasedTable;
 import com.google.common.collect.Table;
-import jakarta.annotation.*;
+import jakarta.annotation.Nullable;
 import java.time.Instant;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
 import org.apache.commons.lang3.*;
 import org.apache.commons.lang3.tuple.Pair;
 

diff --git a/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BQRowResult.java b/underlay/src/main/java/bio/terra/tanagra/query/bigquery/BQRowResult.java
@@ -6,7 +6,7 @@
 import com.google.cloud.bigquery.FieldValue;
 import com.google.cloud.bigquery.FieldValueList;
 import java.sql.Timestamp;
-import java.util.*;
+import java.util.List;
 
 public class BQRowResult implements SqlRowResult {
   private final FieldValueList fieldValues;

diff --git a/underlay/src/main/java/bio/terra/tanagra/query/bigquery/translator/BQApiTranslator.java b/underlay/src/main/java/bio/terra/tanagra/query/bigquery/translator/BQApiTranslator.java
@@ -33,8 +33,10 @@
 import bio.terra.tanagra.query.sql.translator.ApiFilterTranslator;
 import bio.terra.tanagra.query.sql.translator.ApiTranslator;
 import bio.terra.tanagra.underlay.entitymodel.Attribute;
-import jakarta.annotation.*;
-import java.util.*;
+import jakarta.annotation.Nullable;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
 
 public final class BQApiTranslator implements ApiTranslator {
   @Override

diff --git a/...in/java/bio/terra/tanagra/query/bigquery/translator/field/BQAttributeFieldTranslator.java b/...in/java/bio/terra/tanagra/query/bigquery/translator/field/BQAttributeFieldTranslator.java
@@ -12,7 +12,7 @@
 import bio.terra.tanagra.query.sql.translator.ApiFieldTranslator;
 import bio.terra.tanagra.underlay.entitymodel.Attribute;
 import bio.terra.tanagra.underlay.indextable.ITEntityMain;
-import jakarta.annotation.*;
+import jakarta.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.List;
 import java.util.Optional;

diff --git a/underlay/src/main/java/bio/terra/tanagra/query/sql/SqlRowResult.java b/underlay/src/main/java/bio/terra/tanagra/query/sql/SqlRowResult.java
@@ -2,7 +2,7 @@
 
 import bio.terra.tanagra.api.shared.DataType;
 import bio.terra.tanagra.api.shared.Literal;
-import java.util.*;
+import java.util.List;
 
 public interface SqlRowResult {
   /** Get literal value for the column in this row. */

diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/SourceSchema.java b/underlay/src/main/java/bio/terra/tanagra/underlay/SourceSchema.java
@@ -9,7 +9,9 @@
 import bio.terra.tanagra.underlay.sourcetable.*;
 import com.google.common.collect.ImmutableList;
 import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
-import java.util.*;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Optional;
 
 @SuppressFBWarnings(
     value = "NP_UNWRITTEN_PUBLIC_OR_PROTECTED_FIELD",

diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/indextable/ITRelationshipIdPairs.java b/underlay/src/main/java/bio/terra/tanagra/underlay/indextable/ITRelationshipIdPairs.java
@@ -6,8 +6,8 @@
 import bio.terra.tanagra.underlay.serialization.SZBigQuery;
 import bio.terra.tanagra.underlay.sourcetable.*;
 import com.google.common.collect.ImmutableList;
-import java.util.*;
-import java.util.stream.*;
+import java.util.Arrays;
+import java.util.stream.Collectors;
 
 public final class ITRelationshipIdPairs extends IndexTable {
   private static final String TABLE_NAME = "RIDS";

diff --git a/underlay/src/main/java/bio/terra/tanagra/underlay/serialization/SZBigQuery.java b/underlay/src/main/java/bio/terra/tanagra/underlay/serialization/SZBigQuery.java
@@ -2,7 +2,8 @@
 
 import bio.terra.tanagra.annotation.AnnotatedClass;
 import bio.terra.tanagra.annotation.AnnotatedField;
-import java.util.*;
+import java.util.List;
+import java.util.Map;
 
 @AnnotatedClass(
     name = "SZBigQuery",

diff --git a/...src/test/java/bio/terra/tanagra/query/bigquery/resultparsing/BQCountQueryResultsTest.java b/...src/test/java/bio/terra/tanagra/query/bigquery/resultparsing/BQCountQueryResultsTest.java
@@ -23,7 +23,9 @@
 import bio.terra.tanagra.query.bigquery.BQRunnerTest;
 import bio.terra.tanagra.underlay.entitymodel.*;
 import bio.terra.tanagra.underlay.entitymodel.entitygroup.EntityGroup;
-import java.util.*;
+import java.util.List;
+import java.util.Map;
+import java.util.Optional;
 import org.junit.jupiter.api.Test;
 
 public class BQCountQueryResultsTest extends BQRunnerTest {
@@ -213,8 +215,8 @@ void repeatedAttributeField() {
                         .equals(Literal.forString("baz")))
             .findAny();
     assertTrue(bazCount.isPresent());
-    assertTrue(fooCount.get().getCount() == barCount.get().getCount());
-    assertTrue(barCount.get().getCount() == bazCount.get().getCount());
+    assertEquals(fooCount.get().getCount(), barCount.get().getCount());
+    assertEquals(barCount.get().getCount(), bazCount.get().getCount());
   }
 
   @Test