Merge branch 'main' into clone-cohort

annotationProcessor/build.gradle

@@ -3,7 +3,7 @@ plugins {
 
     // These plugins are needed to resolve versions of spring dependencies
     // transitively added by terra-common-lib
-    id 'org.springframework.boot' version '3.3.1'
+    id 'org.springframework.boot' version '3.3.3'
     id 'io.spring.dependency-management' version '1.1.5'
 }
 
@@ -53,8 +53,10 @@ dependencies {
     implementation project(path: ':service')
 
     // explicity declare libs and version to address synk warnings
-    implementation 'org.springframework:spring-web:6.1.12'
-    testFixturesImplementation 'org.springframework:spring-web:6.1.12'
+    implementation "org.springframework:spring-web:${gradle.vSpringWeb}"
+    implementation "org.springframework:spring-webmvc:${gradle.vSpringWeb}"
+    testFixturesImplementation "org.springframework:spring-web:${gradle.vSpringWeb}"
+    testFixturesImplementation "org.springframework:spring-webmvc:${gradle.vSpringWeb}"
 
     // Static analysis
     pmd "net.sourceforge.pmd:pmd-ant:${gradle.vPmd}"

build.gradle

@@ -6,14 +6,15 @@ buildscript {
 }
 
 gradle.ext {
-    vSpringBoot = '3.3.1'
+    vSpringBoot = '3.3.3'
+    vSpringWeb = '6.1.13'
     vPmd = '7.1.0'
     vTerraCommonLib = '1.1.16-SNAPSHOT'
     vApacheCommonsText = '1.12.0'
     vSlf4jApi = '2.0.16'
     vSpotBugs = '4.8.5'
-    vJackson = '2.17.1'
-    vJersey3 = '3.1.7' // Java 17 compatible
+    vJackson = '2.17.2'
+    vJersey = '3.1.8' // Java 17 compatible
     vSwaggerAnnotations = '2.2.22'
     vSwaggerCodegen = '3.0.57'
     vPicocliVersion = '4.7.6'

cli/gradle.lockfile

@@ -3,11 +3,11 @@
 # This file is expected to be part of source control.
 ch.qos.logback:logback-classic:1.5.6=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
 ch.qos.logback:logback-core:1.5.6=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.core:jackson-annotations:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.core:jackson-core:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.core:jackson-databind:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson:jackson-bom:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.core:jackson-annotations:2.17.2=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.core:jackson-core:2.17.2=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.core:jackson-databind:2.17.2=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.17.2=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson:jackson-bom:2.17.2=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
 com.github.oowekyala.ooxml:nice-xml-messages:3.1=pmd
 com.github.spotbugs:spotbugs-annotations:4.8.5=compileClasspath,spotbugs,testCompileClasspath
 com.github.spotbugs:spotbugs:4.8.5=spotbugs

client/build.gradle

@@ -7,7 +7,7 @@ plugins {
     id 'com.jfrog.artifactory' version '5.2.2'
     id 'io.spring.dependency-management' version '1.1.5'
     id 'org.hidetake.swagger.generator' version '2.19.2'
-    id 'org.springframework.boot' version '3.3.1'
+    id 'org.springframework.boot' version '3.3.3'
 }
 
 repositories {
@@ -53,10 +53,10 @@ dependencies {
     implementation "com.fasterxml.jackson.core:jackson-core:${gradle.vJackson}"
     implementation "com.fasterxml.jackson.datatype:jackson-datatype-jsr310:${gradle.vJackson}"
 
-    implementation "org.glassfish.jersey.core:jersey-client:${gradle.vJersey3}"
-    implementation "org.glassfish.jersey.media:jersey-media-json-jackson:${gradle.vJersey3}"
-    implementation "org.glassfish.jersey.media:jersey-media-multipart:${gradle.vJersey3}"
-    implementation "org.glassfish.jersey.connectors:jersey-jdk-connector:${gradle.vJersey3}"
+    implementation "org.glassfish.jersey.core:jersey-client:${gradle.vJersey}"
+    implementation "org.glassfish.jersey.media:jersey-media-json-jackson:${gradle.vJersey}"
+    implementation "org.glassfish.jersey.media:jersey-media-multipart:${gradle.vJersey}"
+    implementation "org.glassfish.jersey.connectors:jersey-jdk-connector:${gradle.vJersey}"
 }
 
 bootJar {

docs/generated/UNDERLAY_CONFIG.md

@@ -73,6 +73,13 @@ When set to true, an indexing job will try to compute a display hint for this at
 
 *Default value:* `false`
 
+### SZAttribute.isDataTypeRepeated
+**optional** boolean
+
+True if the data type is repeated (e.g. an array of ints).
+
+*Default value:* `false`
+
 ### SZAttribute.isSuppressedForExport
 **optional** boolean
 

indexer/gradle.lockfile

@@ -6,13 +6,20 @@ ch.qos.logback:logback-classic:1.5.6=runtimeClasspath,testFixturesRuntimeClasspa
 ch.qos.logback:logback-core:1.5.6=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
 com.charleskorn.kaml:kaml-jvm:0.60.0=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
 com.charleskorn.kaml:kaml:0.60.0=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.core:jackson-annotations:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.core:jackson-core:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.core:jackson-databind:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.datatype:jackson-datatype-joda:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
-com.fasterxml.jackson:jackson-bom:2.17.1=compileClasspath,runtimeClasspath,testCompileClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.core:jackson-annotations:2.17.1=compileClasspath,testCompileClasspath
+com.fasterxml.jackson.core:jackson-annotations:2.17.2=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.core:jackson-core:2.17.1=compileClasspath,testCompileClasspath
+com.fasterxml.jackson.core:jackson-core:2.17.2=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.core:jackson-databind:2.17.1=compileClasspath,testCompileClasspath
+com.fasterxml.jackson.core:jackson-databind:2.17.2=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.17.1=compileClasspath,testCompileClasspath
+com.fasterxml.jackson.dataformat:jackson-dataformat-yaml:2.17.2=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.datatype:jackson-datatype-joda:2.17.1=compileClasspath,testCompileClasspath
+com.fasterxml.jackson.datatype:jackson-datatype-joda:2.17.2=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.17.1=compileClasspath,testCompileClasspath
+com.fasterxml.jackson.datatype:jackson-datatype-jsr310:2.17.2=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
+com.fasterxml.jackson:jackson-bom:2.17.1=compileClasspath,testCompileClasspath
+com.fasterxml.jackson:jackson-bom:2.17.2=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
 com.fasterxml:classmate:1.5.1=runtimeClasspath,testFixturesRuntimeClasspath,testRuntimeClasspath
 com.github.oowekyala.ooxml:nice-xml-messages:3.1=pmd
 com.github.spotbugs:spotbugs-annotations:4.8.5=compileClasspath,spotbugs,testCompileClasspath

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

@@ -47,6 +47,10 @@ public void run(boolean isDryRun) {
                     Field.newBuilder(
                             columnSchema.getColumnName(),
                             BigQueryBeamUtils.fromDataType(columnSchema.getDataType()))
+                        .setMode(
+                            columnSchema.isDataTypeRepeated()
+                                ? Field.Mode.REPEATED
+                                : Field.Mode.NULLABLE)
                         .build())
             .collect(Collectors.toList());
 

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

@@ -92,6 +92,18 @@ public void run(boolean isDryRun) {
                 .collect(Collectors.joining(",", "[", "]")),
             sourceQueryField.getType());
       }
+
+      // Check that the schema repeated flags match those of the index table columns.
+      boolean sourceQueryFieldIsRepeated = sourceQueryField.getMode().equals(Field.Mode.REPEATED);
+      boolean isRepeatedFlagsMatch = attribute.isDataTypeRepeated() == sourceQueryFieldIsRepeated;
+      if (!isRepeatedFlagsMatch) {
+        foundError = true;
+        LOGGER.info(
+            "Data type repeated mismatch found for attribute {}: entity declared {}, SQL schema returns {}",
+            attribute.getName(),
+            attribute.isDataTypeRepeated(),
+            sourceQueryField.getMode());
+      }
     }
     if (foundError) {
       throw new InvalidConfigException("Data type mismatch found for entity: " + entity.getName());