all-of-us · tarekmamdouh · Aug 27, 2025 · Aug 27, 2025 · Aug 27, 2025 · Aug 27, 2025
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -159,7 +159,7 @@ jobs:
           name: Scan dependencies for vulnerabilities
           working_directory: ~/data-browser/public-api
           command: |
-            ./project.rb gradle dependencyCheckAnalyze --info
+            ./gradlew dependencyCheckAnalyze --info
 
   public-ui-build-test:
     <<: *defaults

diff --git a/public-api/build.gradle b/public-api/build.gradle
@@ -8,7 +8,7 @@ buildscript {
         SPRING_FRAMEWORK_VERSION = '6.1.5'
         SPRING_SECURITY_VERSION = '6.2.3'
         LOGBACK_VERSION = '1.5.5'
-        JACKSON_VERSION = '2.16.1'
+        JACKSON_VERSION = '2.18.2'
         SPRING_DEPENDENCY_MANAGEMENT_VERSION = '1.0.13.RELEASE'
         OKHTTP_VERSION = '4.12.0'
         LIQUIBASE_VERSION = '4.27.0'
@@ -37,7 +37,7 @@ plugins {
     id 'idea'
     id 'war'
     id 'org.springframework.boot' version '3.2.0'
-    id 'org.owasp.dependencycheck' version '7.4.4'
+    id 'org.owasp.dependencycheck' version '12.1.0'
     id 'io.spring.dependency-management' version '1.0.13.RELEASE'
     id 'org.hidetake.swagger.generator' version '2.19.2'
     id 'com.google.cloud.tools.appengine-appenginewebxml' version '2.8.0'
@@ -70,7 +70,6 @@ configurations {
     integrationRuntime.extendsFrom testRuntime
     integrationImplementation.extendsFrom implementation
     integrationRuntimeOnly.extendsFrom runtimeOnly
-    __swaggerCodegenV3__
     generatedCompile
     all { exclude group: 'com.google.guava', module: 'guava-jdk5' }
     toolsImplementation.extendsFrom implementation
@@ -174,9 +173,11 @@ repositories {
     mavenCentral()
 }
 
+
+
 dependencies {
+    swaggerCodegen "io.swagger.codegen.v3:swagger-codegen-cli:$project.ext.SWAGGER_3_CODEGEN_VERSION"
     annotationProcessor "org.mapstruct:mapstruct-processor:$project.ext.MAPSTRUCT_VERSION"
-    __swaggerCodegenV3__ "io.swagger.codegen.v3:swagger-codegen-cli:$project.ext.SWAGGER_3_CODEGEN_VERSION"
     generatedCompile "org.springframework.boot:spring-boot-starter-data-rest:$project.ext.SPRING_BOOT_VERSION"
     generatedCompile "org.springframework.boot:spring-boot-starter-validation:$project.ext.SPRING_BOOT_VERSION"
     generatedCompile "com.squareup.okhttp3:okhttp:$project.ext.OKHTTP_VERSION"
@@ -237,7 +238,7 @@ dependencies {
     implementation 'com.google.guava:guava:32.0.1-jre'
     implementation 'com.google.oauth-client:google-oauth-client-jetty:1.34.1'
     implementation 'com.google.protobuf:protobuf-java:3.25.3'
-    implementation 'com.googlecode.owasp-java-html-sanitizer:owasp-java-html-sanitizer:20211018.2'
+    implementation 'com.googlecode.owasp-java-html-sanitizer:owasp-java-html-sanitizer:20240325.1'
     implementation "org.hibernate.orm:hibernate-core:$project.ext.HIBERNATE_VERSION"
     implementation "org.hibernate.orm:hibernate-community-dialects:$project.ext.HIBERNATE_VERSION"
     implementation('org.apache.tomcat:tomcat-jdbc:10.0.23')
@@ -319,7 +320,6 @@ swaggerSources {
     databrowser {
         inputFile = file('src/main/resources/public-api.yaml')
         code {
-            configuration = configurations.__swaggerCodegenV3__
             language = 'spring'
             outputDir = file(SWAGGER_3_CODEGEN_DIR)
             templateDir = file(SWAGGER_TEMPLATE_DIR)
@@ -340,7 +340,6 @@ swaggerSources {
     databrowserApiClient {
         inputFile = file('src/main/resources/public-api.yaml')
         code {
-            configuration = configurations.__swaggerCodegenV3__
             language = 'java'
             outputDir = file(SWAGGER_3_CODEGEN_DIR)
             templateDir = file(SWAGGER_TEMPLATE_DIR)
@@ -361,7 +360,6 @@ swaggerSources {
     workbenchClient {
         inputFile = file('src/main/resources/private-workbench.yaml')
         code {
-            configuration = configurations.__swaggerCodegenV3__
             language = 'java'
             outputDir = file(SWAGGER_3_CODEGEN_DIR)
             templateDir = file(SWAGGER_TEMPLATE_DIR)
@@ -453,7 +451,14 @@ dependencies {
 }
 
 
+dependencyCheck {
+    nvd {
+        apiKey = System.getenv('NVD_API_KEY')
+    }
+}
+
 group = 'org.pmiops.allofus.workbench'
 version = '0.1.0'
 sourceCompatibility = 17
-targetCompatibility = 17
+targetCompatibility = 17
+
diff --git a/public-api/db-cdr/build.gradle b/public-api/db-cdr/build.gradle
@@ -1,6 +1,6 @@
 plugins {
     id 'application'
-    id 'org.liquibase.gradle' version '2.1.1'
+    id 'org.liquibase.gradle' version '2.2.0'
 }
 
 
@@ -31,46 +31,42 @@ dependencies {
 liquibase {
     activities {
         schema {
-            changeLogFile "changelog-schema/db.changelog-master.xml"
+            changelogFile "changelog-schema/db.changelog-master.xml"
             url "jdbc:mysql://${db_host}:${db_port}/${db_name}"
             username "liquibase"
             password "${liquibase_password}"
             classpath "$rootDir"
-            showBanner false
         }
         data {
             if (project.hasProperty('contexts')) {
                 contexts contexts
             }
-            changeLogFile "changelog-data/db.changelog-master.xml"
+            changelogFile "changelog-data/db.changelog-master.xml"
             url "jdbc:mysql://${db_host}:${db_port}/${db_name}"
             username "liquibase"
             password "${liquibase_password}"
             classpath "$rootDir"
-            showBanner false
         }
         add_bigdata_indexes {
             if (project.hasProperty('contexts')) {
                 contexts contexts
             }
-            changeLogFile "changelog-bigdata/db.changelog-add-indexes.xml"
+            changelogFile "changelog-bigdata/db.changelog-add-indexes.xml"
             url "jdbc:mysql://${db_host}:${db_port}/${db_name}"
             username "liquibase"
             password "${liquibase_password}"
             classpath "$rootDir"
-            showBanner false
         }
         drop_bigdata_indexes {
             if (project.hasProperty('contexts')) {
                 contexts contexts
             }
-            changeLogFile "changelog-bigdata/db.changelog-drop-indexes.xml"
+            changelogFile "changelog-bigdata/db.changelog-drop-indexes.xml"
             url "jdbc:mysql://${db_host}:${db_port}/${db_name}"
             username "liquibase"
             password "${liquibase_password}"
             classpath "$rootDir"
-            showBanner false
         }
-        runList = project.ext.runList
+        runList = project.hasProperty('runList') ? project.getProperty('runList') : 'schema'
     }
 }
diff --git a/public-api/db/build.gradle b/public-api/db/build.gradle
@@ -1,6 +1,6 @@
 plugins {
     id 'application'
-    id 'org.liquibase.gradle' version '2.1.1'
+    id 'org.liquibase.gradle' version '2.2.0'
 }
 
 repositories {
@@ -28,11 +28,11 @@ dependencies {
 liquibase {
     activities {
         main {
-            changeLogFile "changelog/db.changelog-master.xml"
+            changelogFile "changelog/db.changelog-master.xml"
             url "jdbc:mysql://${db_host}:${db_port}/databrowser"
             username "liquibase"
             password "${liquibase_password}"
         }
-        runList = project.ext.runList
+        runList = project.hasProperty('runList') ? project.getProperty('runList') : 'main'
     }
 }
diff --git a/public-api/gradle/wrapper/gradle-wrapper.properties b/public-api/gradle/wrapper/gradle-wrapper.properties
@@ -3,4 +3,4 @@ distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-7.6.1-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-8.10.2-bin.zip
diff --git a/public-api/libproject/devstart.rb b/public-api/libproject/devstart.rb
@@ -855,7 +855,7 @@ def update_cdr_config_options(cmd_name, args)
 def update_cdr_config_for_project(cdr_config_file, dry_run)
   common = Common.new
   common.run_inline %W{
-    gradle updateCdrConfig
+    ./gradlew updateCdrConfig
    -PappArgs=['#{cdr_config_file}',#{dry_run}]}
 end
 
@@ -1006,7 +1006,7 @@ def migrate_database(dry_run = false)
   common = Common.new
   common.status "Migrating main database..."
   Dir.chdir("db") do
-    run_inline_or_log(dry_run, %W{gradle --info update -PrunList=main})
+    run_inline_or_log(dry_run, %W{../gradlew update -PrunList=main})
   end
 end
 
@@ -1026,8 +1026,8 @@ def load_config(project, dry_run = false)
 
   common = Common.new
   common.status "Loading #{config_json} into database..."
-  run_inline_or_log(dry_run, %W{gradle --info loadConfig -Pconfig_key=main -Pconfig_file=config/#{config_json}})
-  run_inline_or_log(dry_run, %W{gradle --info loadConfig -Pconfig_key=cdrBigQuerySchema -Pconfig_file=config/cdm/cdm_5_2.json})
+  run_inline_or_log(dry_run, %W{./gradlew loadConfig -Pconfig_key=main -Pconfig_file=config/#{config_json}})
+  run_inline_or_log(dry_run, %W{./gradlew loadConfig -Pconfig_key=cdrBigQuerySchema -Pconfig_file=config/cdm/cdm_5_2.json})
 end
 
 def with_cloud_proxy_and_db(gcc, service_account = nil, key_file = nil)

diff --git a/public-api/settings.gradle b/public-api/settings.gradle
@@ -11,4 +11,4 @@ pluginManagement {
             }
         }
     }
-}
+}
-Original file line number
+Diff line change
@@ Expand Up / @@ -11,4 +11,4 @@ pluginManagement { @@
                 }
             }
         }
-    }
+    }