Util to generateId, remove extra userEmail args (#999)

DataBiosphere · Sep 13, 2024 · 41a32d7 · 41a32d7
1 parent 6a3ee72
commit 41a32d7
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Showing 39 changed files with 291 additions and 360 deletions.
diff --git a/.github/workflows/regression-test.yaml b/.github/workflows/regression-test.yaml
@@ -64,7 +64,7 @@ jobs:
       env:
         TEST_PROJECT_SA_KEY: ${{ secrets.TEST_PROJECT_SA_KEY }}
     - name: Gradle Run Regression Tests Only
-      run: ./gradlew service:regressionTests -PregressionTestUnderlays=cmssynpuf,aouSR2019q4r4 --info --scan
+      run: ./gradlew service:regressionTests -PregressionTestUnderlays=cmssynpuf,aouSR2019q4r4 --scan
       env:
         DBMS: postgresql
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

diff --git a/.github/workflowsForDownstreamRepo/regression-test-downstream-repo.yaml b/.github/workflowsForDownstreamRepo/regression-test-downstream-repo.yaml
@@ -53,7 +53,7 @@ jobs:
         mkdir -p rendered/
         echo "$GHA_SA_KEY" > rendered/gha_sa_key.json
         export GOOGLE_APPLICATION_CREDENTIALS=$PWD/rendered/gha_sa_key.json
-        ./tanagra/gradlew -p tanagra service:regressionTests -PregressionTestUnderlays="${UNDERLAYS:-$DEFAULT_UNDERLAYS}" --info --scan
+        ./tanagra/gradlew -p tanagra service:regressionTests -PregressionTestUnderlays="${UNDERLAYS:-$DEFAULT_UNDERLAYS}" --scan
       env:
         DBMS: postgresql
         GITHUB_TOKEN: ${{ secrets.GITHUB_TOKEN }}

diff --git a/indexer/src/main/java/bio/terra/tanagra/indexing/JobSequencer.java b/indexer/src/main/java/bio/terra/tanagra/indexing/JobSequencer.java
@@ -497,14 +497,11 @@ public enum JobExecutor {
 
     public JobRunner getRunner(
         List<SequencedJobSet> jobSets, boolean isDryRun, IndexingJob.RunType runType) {
-      switch (this) {
-        case SERIAL:
-          return new SerialRunner(jobSets, isDryRun, runType);
-        case PARALLEL:
-          return new ParallelRunner(jobSets, isDryRun, runType);
-        default:
-          throw new IllegalArgumentException("Unknown JobExecution enum type: " + this);
-      }
+      return switch (this) {
+        case SERIAL -> new SerialRunner(jobSets, isDryRun, runType);
+        case PARALLEL -> new ParallelRunner(jobSets, isDryRun, runType);
+        default -> throw new IllegalArgumentException("Unknown JobExecution enum type: " + this);
+      };
     }
   }
 }
diff --git a/service/src/main/java/bio/terra/tanagra/app/controller/CohortsApiController.java b/service/src/main/java/bio/terra/tanagra/app/controller/CohortsApiController.java
@@ -67,8 +67,8 @@ public ResponseEntity<ApiCohort> createCohort(String studyId, ApiCohortCreateInf
             Cohort.builder()
                 .displayName(body.getDisplayName())
                 .description(body.getDescription())
-                .underlay(body.getUnderlayName()),
-            SpringAuthentication.getCurrentUser().getEmail());
+                .underlay(body.getUnderlayName())
+                .createdBy(SpringAuthentication.getCurrentUser().getEmail()));
     return ResponseEntity.ok(ToApiUtils.toApiObject(createdCohort));
   }
 
@@ -195,36 +195,36 @@ public ResponseEntity<ApiInstanceCountList> queryCohortCounts(
 
   private static CohortRevision.CriteriaGroupSection fromApiObject(ApiCriteriaGroupSection apiObj) {
     BooleanAndOrFilter.LogicalOperator operator;
-    JoinOperator joinOperator;
-    switch (apiObj.getOperator()) {
-      case OR:
-        operator = BooleanAndOrFilter.LogicalOperator.OR;
-        joinOperator = null;
-        break;
-      case AND:
-        operator = BooleanAndOrFilter.LogicalOperator.AND;
-        joinOperator = null;
-        break;
-      case DURING_SAME_ENCOUNTER:
-        operator = BooleanAndOrFilter.LogicalOperator.OR;
-        joinOperator = JoinOperator.DURING_SAME_ENCOUNTER;
-        break;
-      case WITHIN_NUM_DAYS:
-        operator = BooleanAndOrFilter.LogicalOperator.OR;
-        joinOperator = JoinOperator.WITHIN_NUM_DAYS;
-        break;
-      case NUM_DAYS_BEFORE:
-        operator = BooleanAndOrFilter.LogicalOperator.OR;
-        joinOperator = JoinOperator.NUM_DAYS_BEFORE;
-        break;
-      case NUM_DAYS_AFTER:
-        operator = BooleanAndOrFilter.LogicalOperator.OR;
-        joinOperator = JoinOperator.NUM_DAYS_AFTER;
-        break;
-      default:
-        throw new IllegalArgumentException(
-            "Unknown criteria group section operator: " + apiObj.getOperator());
-    }
+    JoinOperator joinOperator =
+        switch (apiObj.getOperator()) {
+          case OR -> {
+            operator = BooleanAndOrFilter.LogicalOperator.OR;
+            yield null;
+          }
+          case AND -> {
+            operator = BooleanAndOrFilter.LogicalOperator.AND;
+            yield null;
+          }
+          case DURING_SAME_ENCOUNTER -> {
+            operator = BooleanAndOrFilter.LogicalOperator.OR;
+            yield JoinOperator.DURING_SAME_ENCOUNTER;
+          }
+          case WITHIN_NUM_DAYS -> {
+            operator = BooleanAndOrFilter.LogicalOperator.OR;
+            yield JoinOperator.WITHIN_NUM_DAYS;
+          }
+          case NUM_DAYS_BEFORE -> {
+            operator = BooleanAndOrFilter.LogicalOperator.OR;
+            yield JoinOperator.NUM_DAYS_BEFORE;
+          }
+          case NUM_DAYS_AFTER -> {
+            operator = BooleanAndOrFilter.LogicalOperator.OR;
+            yield JoinOperator.NUM_DAYS_AFTER;
+          }
+          default ->
+              throw new IllegalArgumentException(
+                  "Unknown criteria group section operator: " + apiObj.getOperator());
+        };
 
     return CohortRevision.CriteriaGroupSection.builder()
         .id(apiObj.getId())
@@ -258,15 +258,11 @@ private static CohortRevision.CriteriaGroup fromApiObject(ApiCriteriaGroup apiOb
   }
 
   private static ReducingOperator fromApiObject(ApiReducingOperator apiObj) {
-    switch (apiObj) {
-      case ANY:
-        return null;
-      case FIRST_MENTION_OF:
-        return ReducingOperator.FIRST_MENTION_OF;
-      case LAST_MENTION_OF:
-        return ReducingOperator.LAST_MENTION_OF;
-      default:
-        throw new IllegalArgumentException("Unknown reducing operator: " + apiObj);
-    }
+    return switch (apiObj) {
+      case ANY -> null;
+      case FIRST_MENTION_OF -> ReducingOperator.FIRST_MENTION_OF;
+      case LAST_MENTION_OF -> ReducingOperator.LAST_MENTION_OF;
+      default -> throw new IllegalArgumentException("Unknown reducing operator: " + apiObj);
+    };
   }
 }
diff --git a/service/src/main/java/bio/terra/tanagra/app/controller/ReviewsApiController.java b/service/src/main/java/bio/terra/tanagra/app/controller/ReviewsApiController.java
@@ -147,11 +147,10 @@ public ResponseEntity<ApiReviewList> listReviews(
             offset,
             limit);
     ApiReviewList apiReviews = new ApiReviewList();
+    Cohort cohort = cohortService.getCohort(studyId, cohortId);
     reviewService
         .listReviews(authorizedReviewIds, offset, limit)
-        .forEach(
-            review ->
-                apiReviews.add(toApiObject(review, cohortService.getCohort(studyId, cohortId))));
+        .forEach(review -> apiReviews.add(toApiObject(review, cohort)));
     return ResponseEntity.ok(apiReviews);
   }
 

diff --git a/service/src/main/java/bio/terra/tanagra/app/controller/objmapping/FromApiUtils.java b/service/src/main/java/bio/terra/tanagra/app/controller/objmapping/FromApiUtils.java
@@ -481,18 +481,13 @@ private static ValueDisplayField buildRelationshipField(
   }
 
   public static Literal fromApiObject(ApiLiteral apiLiteral) {
-    switch (apiLiteral.getDataType()) {
-      case INT64:
-        return Literal.forInt64(apiLiteral.getValueUnion().getInt64Val());
-      case STRING:
-        return Literal.forString(apiLiteral.getValueUnion().getStringVal());
-      case BOOLEAN:
-        return Literal.forBoolean(apiLiteral.getValueUnion().isBoolVal());
-      case DATE:
-        return Literal.forDate(apiLiteral.getValueUnion().getDateVal());
-      default:
-        throw new SystemException("Unknown API data type: " + apiLiteral.getDataType());
-    }
+    return switch (apiLiteral.getDataType()) {
+      case INT64 -> Literal.forInt64(apiLiteral.getValueUnion().getInt64Val());
+      case STRING -> Literal.forString(apiLiteral.getValueUnion().getStringVal());
+      case BOOLEAN -> Literal.forBoolean(apiLiteral.getValueUnion().isBoolVal());
+      case DATE -> Literal.forDate(apiLiteral.getValueUnion().getDateVal());
+      default -> throw new SystemException("Unknown API data type: " + apiLiteral.getDataType());
+    };
   }
 
   public static BinaryOperator fromApiObject(ApiBinaryOperator apiOperator) {

diff --git a/service/src/main/java/bio/terra/tanagra/app/controller/objmapping/ToApiUtils.java b/service/src/main/java/bio/terra/tanagra/app/controller/objmapping/ToApiUtils.java
@@ -67,29 +67,28 @@ public static ApiLiteral toApiObject(Literal literal) {
 
     ApiLiteral apiLiteral =
         new ApiLiteral().dataType(ApiDataType.fromValue(literal.getDataType().name()));
-    switch (literal.getDataType()) {
-      case INT64:
-        return apiLiteral.valueUnion(new ApiLiteralValueUnion().int64Val(literal.getInt64Val()));
-      case STRING:
-        return apiLiteral.valueUnion(new ApiLiteralValueUnion().stringVal(literal.getStringVal()));
-      case BOOLEAN:
-        return apiLiteral.valueUnion(new ApiLiteralValueUnion().boolVal(literal.getBooleanVal()));
-      case DATE:
-        return apiLiteral.valueUnion(
-            new ApiLiteralValueUnion()
-                .dateVal(literal.getDateVal() == null ? null : literal.getDateVal().toString()));
-      case TIMESTAMP:
-        return apiLiteral.valueUnion(
-            new ApiLiteralValueUnion()
-                .timestampVal(
-                    literal.getTimestampVal() == null
-                        ? null
-                        : literal.getTimestampVal().toString()));
-      case DOUBLE:
-        return apiLiteral.valueUnion(new ApiLiteralValueUnion().doubleVal(literal.getDoubleVal()));
-      default:
-        throw new SystemException("Unknown data type: " + literal.getDataType());
-    }
+    return switch (literal.getDataType()) {
+      case INT64 ->
+          apiLiteral.valueUnion(new ApiLiteralValueUnion().int64Val(literal.getInt64Val()));
+      case STRING ->
+          apiLiteral.valueUnion(new ApiLiteralValueUnion().stringVal(literal.getStringVal()));
+      case BOOLEAN ->
+          apiLiteral.valueUnion(new ApiLiteralValueUnion().boolVal(literal.getBooleanVal()));
+      case DATE ->
+          apiLiteral.valueUnion(
+              new ApiLiteralValueUnion()
+                  .dateVal(literal.getDateVal() == null ? null : literal.getDateVal().toString()));
+      case TIMESTAMP ->
+          apiLiteral.valueUnion(
+              new ApiLiteralValueUnion()
+                  .timestampVal(
+                      literal.getTimestampVal() == null
+                          ? null
+                          : literal.getTimestampVal().toString()));
+      case DOUBLE ->
+          apiLiteral.valueUnion(new ApiLiteralValueUnion().doubleVal(literal.getDoubleVal()));
+      default -> throw new SystemException("Unknown data type: " + literal.getDataType());
+    };
   }
 
   public static ApiCohort toApiObject(Cohort cohort) {
@@ -215,8 +214,7 @@ private static ApiInstance toApiObject(ListInstance listInstance) {
                         hierarchyFieldSets,
                         ((HierarchyIsMemberField) field).getHierarchy().getName())
                     .setIsMember(value.getValue().getBooleanVal());
-              } else if (field instanceof RelatedEntityIdCountField) {
-                RelatedEntityIdCountField countField = (RelatedEntityIdCountField) field;
+              } else if (field instanceof RelatedEntityIdCountField countField) {
                 relationshipFieldSets.add(
                     new ApiInstanceRelationshipFields()
                         .relatedEntity(countField.getCountedEntity().getName())

diff --git a/service/src/main/java/bio/terra/tanagra/db/CohortDao.java b/service/src/main/java/bio/terra/tanagra/db/CohortDao.java
@@ -327,10 +327,7 @@ public String createNextRevision(
             .setIsMostRecent(true)
             .version(cohort.getMostRecentRevision().getVersion() + 1)
             .createdBy(userEmail)
-            .lastModifiedBy(userEmail)
             .id(null) // Builder will generate a new id.
-            .created(null)
-            .lastModified(null)
             .recordsCount(null) // Only store the records count for frozen revisions.
             .build();
     createRevision(cohortId, nextRevision);

diff --git a/service/src/main/java/bio/terra/tanagra/service/ServiceUtils.java b/service/src/main/java/bio/terra/tanagra/service/ServiceUtils.java
@@ -0,0 +1,11 @@
+package bio.terra.tanagra.service;
+
+import org.apache.commons.lang3.RandomStringUtils;
+
+public class ServiceUtils {
+  private ServiceUtils() {}
+
+  public static String newArtifactId() {
+    return RandomStringUtils.randomAlphanumeric(10);
+  }
+}
diff --git a/service/src/main/java/bio/terra/tanagra/service/UnderlayService.java b/service/src/main/java/bio/terra/tanagra/service/UnderlayService.java
@@ -25,7 +25,6 @@
 import java.util.List;
 import java.util.Map;
 import java.util.Optional;
-import java.util.stream.Collectors;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.stereotype.Component;
 
@@ -65,23 +64,19 @@ public UnderlayService(
 
   public List<Underlay> listUnderlays(ResourceCollection authorizedIds) {
     if (authorizedIds.isAllResources()) {
-      return underlayCache.values().stream()
-          .map(CachedUnderlay::getUnderlay)
-          .collect(Collectors.toUnmodifiableList());
+      return underlayCache.values().stream().map(CachedUnderlay::getUnderlay).toList();
     } else {
       // If the incoming list is empty, the caller does not have permission to see any
       // underlays, so we return an empty list.
       if (authorizedIds.isEmpty()) {
         return Collections.emptyList();
       }
       List<String> authorizedNames =
-          authorizedIds.getResources().stream()
-              .map(ResourceId::getUnderlay)
-              .collect(Collectors.toList());
+          authorizedIds.getResources().stream().map(ResourceId::getUnderlay).toList();
       return underlayCache.values().stream()
           .map(CachedUnderlay::getUnderlay)
           .filter(underlay -> authorizedNames.contains(underlay.getName()))
-          .collect(Collectors.toUnmodifiableList());
+          .toList();
     }
   }