Move Entity/Underlay to EntityFilter

indexer/src/main/java/bio/terra/tanagra/indexing/JobSequencer.java

@@ -8,7 +8,7 @@
 import bio.terra.tanagra.indexing.job.bigquery.WriteChildParent;
 import bio.terra.tanagra.indexing.job.bigquery.WriteEntityAttributes;
 import bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints;
-import bio.terra.tanagra.indexing.job.bigquery.WriteEntitySearchByAttribute;
+import bio.terra.tanagra.indexing.job.bigquery.WriteEntitySearchByAttributes;
 import bio.terra.tanagra.indexing.job.bigquery.WriteRelationshipIntermediateTable;
 import bio.terra.tanagra.indexing.job.bigquery.WriteTextSearchField;
 import bio.terra.tanagra.indexing.job.dataflow.WriteAncestorDescendant;
@@ -29,12 +29,17 @@
 import bio.terra.tanagra.underlay.entitymodel.entitygroup.GroupItems;
 import bio.terra.tanagra.underlay.indextable.ITEntityLevelDisplayHints;
 import bio.terra.tanagra.underlay.indextable.ITEntityMain;
-import bio.terra.tanagra.underlay.indextable.ITEntitySearchByAttribute;
+import bio.terra.tanagra.underlay.indextable.ITEntitySearchByAttributes;
 import bio.terra.tanagra.underlay.indextable.ITHierarchyAncestorDescendant;
 import bio.terra.tanagra.underlay.indextable.ITHierarchyChildParent;
 import bio.terra.tanagra.underlay.indextable.ITRelationshipIdPairs;
 import bio.terra.tanagra.underlay.serialization.SZIndexer;
-import bio.terra.tanagra.underlay.sourcetable.*;
+import bio.terra.tanagra.underlay.sourcetable.STEntityAttributes;
+import bio.terra.tanagra.underlay.sourcetable.STHierarchyChildParent;
+import bio.terra.tanagra.underlay.sourcetable.STHierarchyRootFilter;
+import bio.terra.tanagra.underlay.sourcetable.STRelationshipIdPairs;
+import bio.terra.tanagra.underlay.sourcetable.STRelationshipRollupCounts;
+import bio.terra.tanagra.underlay.sourcetable.STTextSearchTerms;
 import java.util.List;
 import java.util.concurrent.atomic.AtomicBoolean;
 
@@ -72,12 +77,14 @@ public static SequencedJobSet getJobSetForEntity(
           .getOptimizeSearchByAttributes()
           .forEach(
               searchTableAttributes -> {
-                ITEntitySearchByAttribute searchTable =
+                ITEntitySearchByAttributes searchTable =
                     underlay
                         .getIndexSchema()
-                        .getEntitySearchByAttributeTable(entity, searchTableAttributes);
+                        .getEntitySearchByAttributes(
+                            entity,
+                            searchTableAttributes.stream().map(Attribute::getName).toList());
                 jobSet.addJob(
-                    new WriteEntitySearchByAttribute(
+                    new WriteEntitySearchByAttributes(
                         indexerConfig, entity, indexEntityMain, searchTable));
               });
     }

indexer/src/main/java/bio/terra/tanagra/indexing/job/bigquery/WriteEntityLevelDisplayHints.java

@@ -7,7 +7,9 @@
 import bio.terra.tanagra.exception.SystemException;
 import bio.terra.tanagra.indexing.job.BigQueryJob;
 import bio.terra.tanagra.indexing.job.dataflow.beam.BigQueryBeamUtils;
-import bio.terra.tanagra.query.bigquery.*;
+import bio.terra.tanagra.query.bigquery.BQExecutor;
+import bio.terra.tanagra.query.bigquery.BQExecutorInfrastructure;
+import bio.terra.tanagra.query.bigquery.BQTable;
 import bio.terra.tanagra.query.sql.SqlField;
 import bio.terra.tanagra.query.sql.SqlParams;
 import bio.terra.tanagra.query.sql.SqlQueryField;

indexer/src/main/java/bio/terra/tanagra/indexing/job/bigquery/WriteEntitySearchByAttribute.java → indexer/src/main/java/bio/terra/tanagra/indexing/job/bigquery/WriteEntitySearchByAttributes.java

@@ -4,7 +4,7 @@
 import bio.terra.tanagra.indexing.job.dataflow.beam.BigQueryBeamUtils;
 import bio.terra.tanagra.underlay.entitymodel.Entity;
 import bio.terra.tanagra.underlay.indextable.ITEntityMain;
-import bio.terra.tanagra.underlay.indextable.ITEntitySearchByAttribute;
+import bio.terra.tanagra.underlay.indextable.ITEntitySearchByAttributes;
 import bio.terra.tanagra.underlay.serialization.SZIndexer;
 import com.google.cloud.bigquery.Clustering;
 import com.google.cloud.bigquery.Field;
@@ -17,18 +17,18 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-public class WriteEntitySearchByAttribute extends BigQueryJob {
-  private static final Logger LOGGER = LoggerFactory.getLogger(WriteEntitySearchByAttribute.class);
+public class WriteEntitySearchByAttributes extends BigQueryJob {
+  private static final Logger LOGGER = LoggerFactory.getLogger(WriteEntitySearchByAttributes.class);
 
   private final Entity entity;
   private final ITEntityMain entityTable;
-  private final ITEntitySearchByAttribute searchTable;
+  private final ITEntitySearchByAttributes searchTable;
 
-  public WriteEntitySearchByAttribute(
+  public WriteEntitySearchByAttributes(
       SZIndexer indexerConfig,
       Entity entity,
       ITEntityMain entityTable,
-      ITEntitySearchByAttribute searchTable) {
+      ITEntitySearchByAttributes searchTable) {
     super(indexerConfig);
     this.entity = entity;
     this.entityTable = entityTable;

indexer/src/main/java/bio/terra/tanagra/indexing/job/dataflow/WriteRollupCounts.java

@@ -17,7 +17,7 @@
 import bio.terra.tanagra.underlay.indextable.ITHierarchyAncestorDescendant;
 import bio.terra.tanagra.underlay.indextable.ITRelationshipIdPairs;
 import bio.terra.tanagra.underlay.serialization.SZIndexer;
-import bio.terra.tanagra.underlay.sourcetable.*;
+import bio.terra.tanagra.underlay.sourcetable.STRelationshipRollupCounts;
 import com.google.api.services.bigquery.model.TableFieldSchema;
 import com.google.api.services.bigquery.model.TableRow;
 import com.google.api.services.bigquery.model.TableSchema;

service/src/main/java/bio/terra/tanagra/app/controller/CohortsApiController.java

@@ -11,12 +11,18 @@
 import bio.terra.tanagra.api.filter.EntityFilter;
 import bio.terra.tanagra.api.query.PageMarker;
 import bio.terra.tanagra.api.query.count.CountQueryResult;
-import bio.terra.tanagra.api.shared.*;
+import bio.terra.tanagra.api.shared.OrderByDirection;
 import bio.terra.tanagra.app.authentication.SpringAuthentication;
 import bio.terra.tanagra.app.controller.objmapping.FromApiUtils;
 import bio.terra.tanagra.app.controller.objmapping.ToApiUtils;
 import bio.terra.tanagra.generated.controller.CohortsApi;
-import bio.terra.tanagra.generated.model.*;
+import bio.terra.tanagra.generated.model.ApiCohort;
+import bio.terra.tanagra.generated.model.ApiCohortCloneInfo;
+import bio.terra.tanagra.generated.model.ApiCohortCountQuery;
+import bio.terra.tanagra.generated.model.ApiCohortCreateInfo;
+import bio.terra.tanagra.generated.model.ApiCohortList;
+import bio.terra.tanagra.generated.model.ApiCohortUpdateInfo;
+import bio.terra.tanagra.generated.model.ApiInstanceCountList;
 import bio.terra.tanagra.service.UnderlayService;
 import bio.terra.tanagra.service.accesscontrol.AccessControlService;
 import bio.terra.tanagra.service.accesscontrol.Permissions;

service/src/main/java/bio/terra/tanagra/app/controller/ReviewsApiController.java

@@ -46,7 +46,7 @@
 import bio.terra.tanagra.service.artifact.reviewquery.ReviewQueryOrderBy;
 import bio.terra.tanagra.service.artifact.reviewquery.ReviewQueryRequest;
 import bio.terra.tanagra.service.artifact.reviewquery.ReviewQueryResult;
-import bio.terra.tanagra.service.filter.*;
+import bio.terra.tanagra.service.filter.FilterBuilderService;
 import bio.terra.tanagra.underlay.Underlay;
 import bio.terra.tanagra.underlay.entitymodel.Attribute;
 import bio.terra.tanagra.underlay.entitymodel.Entity;

service/src/main/java/bio/terra/tanagra/app/controller/objmapping/FromApiUtils.java

@@ -7,7 +7,21 @@
 import bio.terra.tanagra.api.field.HierarchyPathField;
 import bio.terra.tanagra.api.field.RelatedEntityIdCountField;
 import bio.terra.tanagra.api.field.ValueDisplayField;
-import bio.terra.tanagra.api.filter.*;
+import bio.terra.tanagra.api.filter.AttributeFilter;
+import bio.terra.tanagra.api.filter.BooleanAndOrFilter;
+import bio.terra.tanagra.api.filter.BooleanNotFilter;
+import bio.terra.tanagra.api.filter.EntityFilter;
+import bio.terra.tanagra.api.filter.GroupHasItemsFilter;
+import bio.terra.tanagra.api.filter.HierarchyHasAncestorFilter;
+import bio.terra.tanagra.api.filter.HierarchyHasParentFilter;
+import bio.terra.tanagra.api.filter.HierarchyIsLeafFilter;
+import bio.terra.tanagra.api.filter.HierarchyIsMemberFilter;
+import bio.terra.tanagra.api.filter.HierarchyIsRootFilter;
+import bio.terra.tanagra.api.filter.ItemInGroupFilter;
+import bio.terra.tanagra.api.filter.OccurrenceForPrimaryFilter;
+import bio.terra.tanagra.api.filter.PrimaryWithCriteriaFilter;
+import bio.terra.tanagra.api.filter.RelationshipFilter;
+import bio.terra.tanagra.api.filter.TextSearchFilter;
 import bio.terra.tanagra.api.query.PageMarker;
 import bio.terra.tanagra.api.query.list.ListQueryRequest;
 import bio.terra.tanagra.api.query.list.OrderBy;

service/src/main/java/bio/terra/tanagra/app/controller/objmapping/ToApiUtils.java

@@ -10,9 +10,31 @@
 import bio.terra.tanagra.api.query.count.CountQueryResult;
 import bio.terra.tanagra.api.query.list.ListInstance;
 import bio.terra.tanagra.api.query.list.ListQueryResult;
-import bio.terra.tanagra.api.shared.*;
+import bio.terra.tanagra.api.shared.Literal;
+import bio.terra.tanagra.api.shared.ReducingOperator;
+import bio.terra.tanagra.api.shared.ValueDisplay;
 import bio.terra.tanagra.exception.SystemException;
-import bio.terra.tanagra.generated.model.*;
+import bio.terra.tanagra.generated.model.ApiAnnotationValue;
+import bio.terra.tanagra.generated.model.ApiAttribute;
+import bio.terra.tanagra.generated.model.ApiCohort;
+import bio.terra.tanagra.generated.model.ApiCriteria;
+import bio.terra.tanagra.generated.model.ApiCriteriaGroup;
+import bio.terra.tanagra.generated.model.ApiCriteriaGroupSection;
+import bio.terra.tanagra.generated.model.ApiDataType;
+import bio.terra.tanagra.generated.model.ApiInstance;
+import bio.terra.tanagra.generated.model.ApiInstanceCount;
+import bio.terra.tanagra.generated.model.ApiInstanceCountList;
+import bio.terra.tanagra.generated.model.ApiInstanceHierarchyFields;
+import bio.terra.tanagra.generated.model.ApiInstanceListResult;
+import bio.terra.tanagra.generated.model.ApiInstanceRelationshipFields;
+import bio.terra.tanagra.generated.model.ApiLiteral;
+import bio.terra.tanagra.generated.model.ApiLiteralValueUnion;
+import bio.terra.tanagra.generated.model.ApiProperties;
+import bio.terra.tanagra.generated.model.ApiPropertyKeyValue;
+import bio.terra.tanagra.generated.model.ApiReducingOperator;
+import bio.terra.tanagra.generated.model.ApiStudy;
+import bio.terra.tanagra.generated.model.ApiUnderlaySummary;
+import bio.terra.tanagra.generated.model.ApiValueDisplay;
 import bio.terra.tanagra.service.artifact.model.AnnotationValue;
 import bio.terra.tanagra.service.artifact.model.Cohort;
 import bio.terra.tanagra.service.artifact.model.CohortRevision;

service/src/main/java/bio/terra/tanagra/db/CohortDao.java

@@ -5,7 +5,8 @@
 import bio.terra.common.exception.MissingRequiredFieldException;
 import bio.terra.common.exception.NotFoundException;
 import bio.terra.tanagra.api.filter.BooleanAndOrFilter;
-import bio.terra.tanagra.api.shared.*;
+import bio.terra.tanagra.api.shared.JoinOperator;
+import bio.terra.tanagra.api.shared.ReducingOperator;
 import bio.terra.tanagra.exception.SystemException;
 import bio.terra.tanagra.service.artifact.model.Cohort;
 import bio.terra.tanagra.service.artifact.model.CohortRevision;

service/src/main/java/bio/terra/tanagra/service/UnderlayService.java

@@ -1,6 +1,13 @@
 package bio.terra.tanagra.service;
 
-import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.*;
+import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.ENUM_COUNT_ALIAS;
+import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.ENUM_DISP_ALIAS;
+import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.ENUM_VAL_ALIAS;
+import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.MAX_VAL_ALIAS;
+import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.MIN_VAL_ALIAS;
+import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.isEnumHintForRepeatedStringValue;
+import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.isEnumHintForValueDisplay;
+import static bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints.isRangeHint;
 
 import bio.terra.common.exception.NotFoundException;
 import bio.terra.tanagra.api.field.AttributeField;
@@ -16,7 +23,8 @@
 import bio.terra.tanagra.api.shared.Literal;
 import bio.terra.tanagra.api.shared.OrderByDirection;
 import bio.terra.tanagra.api.shared.ValueDisplay;
-import bio.terra.tanagra.app.configuration.*;
+import bio.terra.tanagra.app.configuration.ExportConfiguration;
+import bio.terra.tanagra.app.configuration.UnderlayConfiguration;
 import bio.terra.tanagra.indexing.job.bigquery.WriteEntityLevelDisplayHints;
 import bio.terra.tanagra.query.bigquery.translator.BQApiTranslator;
 import bio.terra.tanagra.query.sql.SqlParams;
@@ -26,8 +34,9 @@
 import bio.terra.tanagra.service.accesscontrol.ResourceId;
 import bio.terra.tanagra.underlay.ConfigReader;
 import bio.terra.tanagra.underlay.Underlay;
-import bio.terra.tanagra.underlay.entitymodel.*;
-import bio.terra.tanagra.underlay.serialization.*;
+import bio.terra.tanagra.underlay.entitymodel.Entity;
+import bio.terra.tanagra.underlay.serialization.SZService;
+import bio.terra.tanagra.underlay.serialization.SZUnderlay;
 import com.google.common.collect.ImmutableMap;
 import jakarta.annotation.Nullable;
 import java.util.ArrayList;

service/src/main/java/bio/terra/tanagra/service/accesscontrol/model/FineGrainedAccessControl.java

@@ -1,6 +1,9 @@
 package bio.terra.tanagra.service.accesscontrol.model;
 
-import bio.terra.tanagra.service.accesscontrol.*;
+import bio.terra.tanagra.service.accesscontrol.AccessControlHelper;
+import bio.terra.tanagra.service.accesscontrol.Permissions;
+import bio.terra.tanagra.service.accesscontrol.ResourceCollection;
+import bio.terra.tanagra.service.accesscontrol.ResourceId;
 import bio.terra.tanagra.service.authentication.UserId;
 import java.util.List;
 

service/src/main/java/bio/terra/tanagra/service/artifact/model/Cohort.java

@@ -2,7 +2,7 @@
 
 import static bio.terra.tanagra.service.artifact.model.Study.MAX_DISPLAY_NAME_LENGTH;
 
-import bio.terra.common.exception.*;
+import bio.terra.common.exception.BadRequestException;
 import bio.terra.tanagra.exception.SystemException;
 import jakarta.annotation.Nullable;
 import java.time.OffsetDateTime;

service/src/main/java/bio/terra/tanagra/service/artifact/model/CohortRevision.java

@@ -2,7 +2,8 @@
 
 import bio.terra.common.exception.NotFoundException;
 import bio.terra.tanagra.api.filter.BooleanAndOrFilter;
-import bio.terra.tanagra.api.shared.*;
+import bio.terra.tanagra.api.shared.JoinOperator;
+import bio.terra.tanagra.api.shared.ReducingOperator;
 import jakarta.annotation.Nullable;
 import java.time.OffsetDateTime;
 import java.util.ArrayList;

service/src/main/java/bio/terra/tanagra/service/artifact/model/FeatureSet.java

@@ -2,7 +2,7 @@
 
 import static bio.terra.tanagra.service.artifact.model.Study.MAX_DISPLAY_NAME_LENGTH;
 
-import bio.terra.common.exception.*;
+import bio.terra.common.exception.BadRequestException;
 import bio.terra.tanagra.underlay.entitymodel.Entity;
 import jakarta.annotation.Nullable;
 import java.time.OffsetDateTime;

service/src/main/java/bio/terra/tanagra/service/artifact/model/Review.java

@@ -2,7 +2,7 @@
 
 import static bio.terra.tanagra.service.artifact.model.Study.MAX_DISPLAY_NAME_LENGTH;
 
-import bio.terra.common.exception.*;
+import bio.terra.common.exception.BadRequestException;
 import jakarta.annotation.Nullable;
 import java.time.OffsetDateTime;
 

service/src/main/java/bio/terra/tanagra/service/artifact/model/Study.java

@@ -1,6 +1,6 @@
 package bio.terra.tanagra.service.artifact.model;
 
-import bio.terra.common.exception.*;
+import bio.terra.common.exception.BadRequestException;
 import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
 import com.fasterxml.jackson.databind.annotation.JsonPOJOBuilder;
 import jakarta.annotation.Nullable;

service/src/main/java/bio/terra/tanagra/service/export/impl/IpynbFileDownload.java

@@ -1,6 +1,6 @@
 package bio.terra.tanagra.service.export.impl;
 
-import bio.terra.tanagra.api.query.export.*;
+import bio.terra.tanagra.api.query.export.ExportQueryResult;
 import bio.terra.tanagra.exception.SystemException;
 import bio.terra.tanagra.service.export.DataExport;
 import bio.terra.tanagra.service.export.DataExportHelper;

service/src/main/java/bio/terra/tanagra/service/export/impl/RegressionTest.java

@@ -2,7 +2,7 @@
 
 import static bio.terra.tanagra.utils.NameUtils.simplifyStringForName;
 
-import bio.terra.tanagra.api.query.export.*;
+import bio.terra.tanagra.api.query.export.ExportQueryResult;
 import bio.terra.tanagra.proto.regressiontest.RTCohort;
 import bio.terra.tanagra.proto.regressiontest.RTCriteria;
 import bio.terra.tanagra.proto.regressiontest.RTDataFeatureSet;

service/src/main/java/bio/terra/tanagra/service/export/impl/VwbFileExport.java

@@ -2,7 +2,7 @@
 
 import static bio.terra.tanagra.service.export.DataExportHelper.urlEncode;
 
-import bio.terra.tanagra.api.query.export.*;
+import bio.terra.tanagra.api.query.export.ExportQueryResult;
 import bio.terra.tanagra.service.export.DataExport;
 import bio.terra.tanagra.service.export.DataExportHelper;
 import bio.terra.tanagra.service.export.DeploymentConfig;

service/src/main/java/bio/terra/tanagra/service/filter/FilterBuilderService.java

@@ -2,9 +2,18 @@
 
 import bio.terra.tanagra.api.field.AttributeField;
 import bio.terra.tanagra.api.field.ValueDisplayField;
-import bio.terra.tanagra.api.filter.*;
+import bio.terra.tanagra.api.filter.AttributeFilter;
+import bio.terra.tanagra.api.filter.BooleanAndOrFilter;
 import bio.terra.tanagra.api.filter.BooleanAndOrFilter.LogicalOperator;
-import bio.terra.tanagra.api.shared.*;
+import bio.terra.tanagra.api.filter.BooleanNotFilter;
+import bio.terra.tanagra.api.filter.EntityFilter;
+import bio.terra.tanagra.api.filter.GroupHasItemsFilter;
+import bio.terra.tanagra.api.filter.ItemInGroupFilter;
+import bio.terra.tanagra.api.filter.OccurrenceForPrimaryFilter;
+import bio.terra.tanagra.api.filter.RelationshipFilter;
+import bio.terra.tanagra.api.filter.TemporalPrimaryFilter;
+import bio.terra.tanagra.api.shared.BinaryOperator;
+import bio.terra.tanagra.api.shared.Literal;
 import bio.terra.tanagra.exception.InvalidQueryException;
 import bio.terra.tanagra.exception.SystemException;
 import bio.terra.tanagra.filterbuilder.EntityOutput;
@@ -21,7 +30,9 @@
 import bio.terra.tanagra.underlay.entitymodel.entitygroup.CriteriaOccurrence;
 import bio.terra.tanagra.underlay.entitymodel.entitygroup.EntityGroup;
 import bio.terra.tanagra.underlay.entitymodel.entitygroup.GroupItems;
-import bio.terra.tanagra.underlay.uiplugin.*;
+import bio.terra.tanagra.underlay.uiplugin.CriteriaSelector;
+import bio.terra.tanagra.underlay.uiplugin.PrepackagedCriteria;
+import bio.terra.tanagra.underlay.uiplugin.SelectionData;
 import jakarta.annotation.Nullable;
 import java.util.ArrayList;
 import java.util.HashMap;

service/src/test/java/bio/terra/tanagra/service/CohortServiceTest.java

@@ -13,7 +13,8 @@
 import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
-import bio.terra.common.exception.*;
+import bio.terra.common.exception.BadRequestException;
+import bio.terra.common.exception.NotFoundException;
 import bio.terra.tanagra.api.shared.DataType;
 import bio.terra.tanagra.api.shared.Literal;
 import bio.terra.tanagra.app.Main;

service/src/test/java/bio/terra/tanagra/service/FeatureSetServiceTest.java

@@ -10,15 +10,18 @@
 import static org.junit.jupiter.api.Assertions.assertThrows;
 import static org.junit.jupiter.api.Assertions.assertTrue;
 
-import bio.terra.common.exception.*;
+import bio.terra.common.exception.BadRequestException;
+import bio.terra.common.exception.NotFoundException;
 import bio.terra.tanagra.app.Main;
 import bio.terra.tanagra.service.accesscontrol.Permissions;
 import bio.terra.tanagra.service.accesscontrol.ResourceCollection;
 import bio.terra.tanagra.service.accesscontrol.ResourceId;
 import bio.terra.tanagra.service.accesscontrol.ResourceType;
 import bio.terra.tanagra.service.artifact.FeatureSetService;
 import bio.terra.tanagra.service.artifact.StudyService;
-import bio.terra.tanagra.service.artifact.model.*;
+import bio.terra.tanagra.service.artifact.model.Criteria;
+import bio.terra.tanagra.service.artifact.model.FeatureSet;
+import bio.terra.tanagra.service.artifact.model.Study;
 import java.util.Comparator;
 import java.util.List;
 import java.util.Map;