diff --git a/.github/workflows/ecr.yml b/.github/workflows/ecr.yml
index 8746cd4b..90b40339 100644
--- a/.github/workflows/ecr.yml
+++ b/.github/workflows/ecr.yml
@@ -6,6 +6,7 @@ on:
   push:
     branches:
       - develop
+      - ja-iss-14-drs-manifests # remove after confirming this works
 permissions:
   id-token: write
 jobs:
@@ -45,8 +46,20 @@ jobs:
         with:
           registry: ${{ secrets.AWS_ACCOUNT_ID }}.dkr.ecr.${{ secrets.AWS_REGION }}.amazonaws.com
 
-      - name: Build and push to ECR
-        id: build-and-push-to-ecr
+      - name: Build and push app to ECR
+        id: build-and-push-app-to-ecr
+        uses: docker/build-push-action@v6
+        with:
+          context: .
+          platforms: linux/amd64,linux/arm64
+          push: true
+          tags: |
+            ${{ secrets.AWS_ACCOUNT_ID }}.dkr.ecr.${{ secrets.AWS_REGION }}.amazonaws.com/${{ env.DOCKER_REPO }}:${{ env.DOCKER_TAG }}
+            ${{ secrets.AWS_ACCOUNT_ID }}.dkr.ecr.${{ secrets.AWS_REGION }}.amazonaws.com/${{ env.DOCKER_REPO }}:develop
+            ${{ secrets.AWS_ACCOUNT_ID }}.dkr.ecr.${{ secrets.AWS_REGION }}.amazonaws.com/${{ env.DOCKER_REPO }}:latest
+
+      - name: Build and push liquibase to ECR
+        id: build-and-push-liquibase-to-ecr
         uses: docker/build-push-action@v6
         with:
           context: liquibase
diff --git a/Dockerfile b/Dockerfile
index e68c4481..3865754a 100644
--- a/Dockerfile
+++ b/Dockerfile
@@ -1,63 +1,24 @@
-##################################################
-# BUILDER CONTAINER
-##################################################
+FROM gradle:9.5.1-jdk25-corretto AS builder
 
-FROM openjdk:11.0.12 as builder
+WORKDIR /home/gradle/project
 
-USER root
+COPY --chown=gradle:gradle build.gradle* settings.gradle* ./
+COPY --chown=gradle:gradle src ./src
 
-WORKDIR /usr/src/dependencies
+RUN gradle build -x test --no-daemon
 
-# INSTALL MAKE
-RUN apt update \
-    && apt install build-essential -y
+FROM amazoncorretto:25.0.3-alpine
 
-# INSTALL SQLITE3
-RUN wget https://www.sqlite.org/2021/sqlite-autoconf-3340100.tar.gz \
-    && tar -zxf sqlite-autoconf-3340100.tar.gz \
-    && cd sqlite-autoconf-3340100 \
-    && ./configure \
-    && make \
-    && make install
+RUN addgroup -S appgroup && adduser -S appuser -G appgroup
 
-# USER 'make' and 'sqlite3' to create the dev database
-COPY Makefile Makefile
-COPY database/sqlite database/sqlite
-RUN make sqlite-db-refresh
+WORKDIR /app
 
-##################################################
-# GRADLE CONTAINER
-##################################################
+COPY --from=builder /home/gradle/project/build/libs/*.jar app.jar
 
-FROM gradle:7.3.3-jdk11 as gradleimage
+RUN chown -R appuser:appgroup /app
 
-WORKDIR /home/gradle/source
+USER appuser
 
-COPY build.gradle build.gradle
-COPY gradlew gradlew
-COPY settings.gradle settings.gradle
-COPY src src
-COPY src/main/resources/application.yml /app/application.yml
+EXPOSE 8080
 
-RUN gradle wrapper
-
-RUN ./gradlew bootJar
-
-##################################################
-# FINAL CONTAINER
-##################################################
-
-FROM adoptopenjdk/openjdk12:jre-12.0.2_10-alpine
-
-USER root
-
-ARG VERSION
-
-WORKDIR /usr/src/app
-
-# copy jar, dev db, and dev resource files
-COPY --from=gradleimage /home/gradle/source/build/libs/ga4gh-starter-kit-drs-${VERSION}.jar ga4gh-starter-kit-drs.jar
-COPY --from=builder /usr/src/dependencies/ga4gh-starter-kit.dev.db ga4gh-starter-kit.dev.db
-COPY src/test/resources/ src/test/resources/
-
-ENTRYPOINT ["java", "-jar", "ga4gh-starter-kit-drs.jar"]
+ENTRYPOINT ["java", "-jar", "app.jar"]
diff --git a/deprecated/starterkit/drs/app/DrsServer.java b/deprecated/starterkit/drs/app/DrsServer.java
deleted file mode 100644
index 693fc00d..00000000
--- a/deprecated/starterkit/drs/app/DrsServer.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package org.ga4gh.starterkit.drs.app;
-
-import org.apache.commons.cli.Options;
-import org.ga4gh.starterkit.common.util.webserver.ServerPropertySetter;
-import org.springframework.boot.SpringApplication;
-import org.springframework.boot.autoconfigure.SpringBootApplication;
-import org.springframework.context.annotation.ComponentScan;
-
-/**
- * Contains main method for running a standalone DRS deployment as a Spring Boot
- * application
- */
-@SpringBootApplication
-@ComponentScan(basePackages = "org.ga4gh.starterkit.drs")
-public class DrsServer {
-
-    /**
-     * Run the DRS standalone server as a Spring Boot application.
-     * @param args command line arguments
-     */
-    public static void main(String[] args) {
-        boolean setupSuccess = setup(args);
-        if (setupSuccess) {
-            try {
-                SpringApplication.run(DrsServer.class, args);
-            } catch (Exception ex) {
-                ex.printStackTrace();
-            }
-        } else {
-            System.out.println("Application failed at initial setup phase, this is likely an error in the YAML config file. Exiting");
-        }
-    }
-
-    private static boolean setup(String[] args) {
-        Options options = new DrsServerSpringConfig().getCommandLineOptions();
-        ServerPropertySetter setter = new ServerPropertySetter();
-        return setter.setServerProperties(DrsServerYamlConfigContainer.class, args, options, "config");
-    }
-}
diff --git a/deprecated/starterkit/drs/app/DrsServerConstants.java b/deprecated/starterkit/drs/app/DrsServerConstants.java
deleted file mode 100644
index 02e52450..00000000
--- a/deprecated/starterkit/drs/app/DrsServerConstants.java
+++ /dev/null
@@ -1,39 +0,0 @@
-package org.ga4gh.starterkit.drs.app;
-
-/**
- * String constants for deployment config, generally Spring bean name/qualifier
- * constants
- */
-public class DrsServerConstants {
-
-    /* Spring bean names - DRS config container */
-
-    /**
-     * Spring bean qualifier for an empty drs config container
-     */
-    public static final String EMPTY_DRS_CONFIG_CONTAINER = "emptyDrsConfigContainer";
-
-    /**
-     * Spring bean qualifier for the drs config container containing all defaults
-     */
-    public static final String DEFAULT_DRS_CONFIG_CONTAINER = "defaultDrsConfigContainer";
-
-    /**
-     * Spring bean qualifier for the drs config container containing user-loaded properties
-     */
-    public static final String USER_DRS_CONFIG_CONTAINER = "userDrsConfigContainer";
-
-    /**
-     * Spring bean qualifier for the final drs config container containing merged
-     * properties from default and user-loaded (user-loaded properties override
-     * defaults) 
-     */
-    public static final String FINAL_DRS_CONFIG_CONTAINER = "finalDrsConfigContainer";
-
-    /* Spring bean scope */
-
-    /**
-     * Indicates Spring bean has 'prototype' lifecycle
-     */
-    public static final String PROTOTYPE = "prototype";
-}
diff --git a/deprecated/starterkit/drs/app/DrsServerSpringConfig.java b/deprecated/starterkit/drs/app/DrsServerSpringConfig.java
deleted file mode 100644
index 789a52a1..00000000
--- a/deprecated/starterkit/drs/app/DrsServerSpringConfig.java
+++ /dev/null
@@ -1,336 +0,0 @@
-package org.ga4gh.starterkit.drs.app;
-
-import org.apache.catalina.connector.Connector;
-import org.apache.commons.cli.*;
-import org.ga4gh.starterkit.common.config.DatabaseProps;
-import org.ga4gh.starterkit.common.config.ServerProps;
-import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
-import org.ga4gh.starterkit.common.util.CliYamlConfigLoader;
-import org.ga4gh.starterkit.common.util.DeepObjectMerger;
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
-import org.ga4gh.starterkit.common.util.webserver.AdminEndpointsConnector;
-import org.ga4gh.starterkit.common.util.webserver.AdminEndpointsFilter;
-import org.ga4gh.starterkit.common.util.webserver.CorsFilterBuilder;
-import org.ga4gh.starterkit.common.util.webserver.TomcatMultiConnectorServletWebServerFactoryCustomizer;
-import org.ga4gh.starterkit.drs.config.DrsServiceProps;
-import org.ga4gh.starterkit.drs.exception.DrsCustomExceptionHandling;
-import org.ga4gh.starterkit.drs.model.*;
-import org.ga4gh.starterkit.drs.utils.cache.AccessCache;
-import org.ga4gh.starterkit.drs.utils.hibernate.DrsHibernateUtil;
-import org.ga4gh.starterkit.drs.utils.passport.UserPassportMapVerifier;
-import org.ga4gh.starterkit.drs.utils.requesthandler.AccessRequestHandler;
-import org.ga4gh.starterkit.drs.utils.requesthandler.AuthInfoRequestHandler;
-import org.ga4gh.starterkit.drs.utils.requesthandler.FileStreamRequestHandler;
-import org.ga4gh.starterkit.drs.utils.requesthandler.ObjectRequestHandler;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.beans.factory.annotation.Qualifier;
-import org.springframework.beans.factory.annotation.Value;
-import org.springframework.boot.ApplicationArguments;
-import org.springframework.boot.autoconfigure.web.ServerProperties;
-import org.springframework.boot.context.properties.ConfigurationProperties;
-import org.springframework.boot.web.server.WebServerFactoryCustomizer;
-import org.springframework.boot.web.servlet.FilterRegistrationBean;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-import org.springframework.context.annotation.Scope;
-import org.springframework.web.context.annotation.RequestScope;
-import org.springframework.web.filter.CorsFilter;
-
-import java.io.Serializable;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Contains Spring bean definitions that are to be loaded for the DRS service
- * under all deployment contexts (ie as part of both standalone and GA4GH
- * multi-API service deployments)
- * 
- * @see org.ga4gh.starterkit.drs.app.DrsStandaloneSpringConfig Spring config beans used only during standalone deployments
- */
-@Configuration
-@ConfigurationProperties
-public class DrsServerSpringConfig {
-
-    /* ******************************
-     * TOMCAT SERVER
-     * ****************************** */
-
-    @Value("${server.admin.port:4501}")
-    private String serverAdminPort;
-
-    @Bean
-    public WebServerFactoryCustomizer servletContainer() {
-        Connector[] additionalConnectors = AdminEndpointsConnector.additionalConnector(serverAdminPort);
-        ServerProperties serverProperties = new ServerProperties();
-        return new TomcatMultiConnectorServletWebServerFactoryCustomizer(serverProperties, additionalConnectors);
-    }
-
-    @Bean
-    public FilterRegistrationBean<AdminEndpointsFilter> adminEndpointsFilter() {
-        return new FilterRegistrationBean<AdminEndpointsFilter>(new AdminEndpointsFilter(Integer.valueOf(serverAdminPort)));
-    }
-    
-    @Bean
-    public DrsCustomExceptionHandling customExceptionHandling() {
-        return new DrsCustomExceptionHandling();
-    }
-
-    @Bean
-    public FilterRegistrationBean<CorsFilter> corsFilter(
-        @Autowired ServerProps serverProps
-    ) {
-        return new CorsFilterBuilder(serverProps).buildFilter();
-    }
-
-    /* ******************************
-     * YAML CONFIG
-     * ****************************** */
-
-    /**
-     * Load command line options object, to enable parsing of program args
-     * @return valid command line options to be parsed
-     */
-    @Bean
-    public Options getCommandLineOptions() {
-        final Options options = new Options();
-        options.addOption("c", "config", true, "Path to DRS YAML config file");
-        return options;
-    }
-
-    /**
-     * Loads an empty DRS config container
-     * @return DRS config container with empty properties
-     */
-    @Bean
-    @Scope(DrsServerConstants.PROTOTYPE)
-    @Qualifier(DrsServerConstants.EMPTY_DRS_CONFIG_CONTAINER)
-    public DrsServerYamlConfigContainer emptyDrsConfigContainer() {
-        return new DrsServerYamlConfigContainer(new DrsServerYamlConfig());
-    }
-
-    /**
-     * Loads a DRS config container singleton containing all default properties
-     * @return DRS config container containing defaults
-     */
-    @Bean
-    @Qualifier(DrsServerConstants.DEFAULT_DRS_CONFIG_CONTAINER)
-    public DrsServerYamlConfigContainer defaultDrsConfigContainer() {
-        return new DrsServerYamlConfigContainer(new DrsServerYamlConfig());
-    }
-
-    public static boolean validateArguments(ApplicationArguments args, String optionName) {
-        try {
-            Options options = new Options();
-            options.addOption(Option.builder("c")
-                    .longOpt(optionName)
-                    .hasArg()
-                    .desc("Path to configuration file")
-                    .build());
-
-            CommandLineParser parser = new DefaultParser();
-            parser.parse(options, args.getSourceArgs());
-            return true;
-        } catch (ParseException e) {
-            System.out.println("ERROR: Invalid arguments: " + e.getMessage());
-            return false;
-        }
-    }
-
-    /**
-     * Loads a DRS config container singleton containing user-specified properties (via config file)
-     * @param args command line args
-     * @param options valid set of command line options to be parsed
-     * @param drsConfigContainer empty DRS config container
-     * @return DRS config container singleton containing user-specified properties
-     */
-    @Bean
-    @Qualifier(DrsServerConstants.USER_DRS_CONFIG_CONTAINER)
-    public DrsServerYamlConfigContainer runtimeDrsConfigContainer(
-        @Autowired ApplicationArguments args,
-        @Autowired() Options options,
-        @Qualifier(DrsServerConstants.EMPTY_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer drsConfigContainer
-    ) {
-        if (!validateArguments(args, "config")) {
-            System.exit(1); // Exit if validation fails
-        }
-
-        DrsServerYamlConfigContainer userConfigContainer = CliYamlConfigLoader.load(DrsServerYamlConfigContainer.class, args, options, "config");
-        if (userConfigContainer != null) {
-            return userConfigContainer;
-        }
-        return drsConfigContainer;
-    }
-
-    /**
-     * Loads the final DRS config container singleton containing merged properties
-     * between default and user-specified
-     * @param defaultContainer contains default properties
-     * @param userContainer contains user-specified properties
-     * @return contains merged properties
-     */
-    @Bean
-    @Qualifier(DrsServerConstants.FINAL_DRS_CONFIG_CONTAINER)
-    public DrsServerYamlConfigContainer mergedDrsConfigContainer(
-        @Qualifier(DrsServerConstants.DEFAULT_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer defaultContainer,
-        @Qualifier(DrsServerConstants.USER_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer userContainer
-    ) {
-        DeepObjectMerger merger = new DeepObjectMerger();
-        merger.merge(userContainer, defaultContainer);
-        return defaultContainer;
-    }
-
-    /**
-     * Retrieve server props object from merged DRS config container
-     * @param drsConfigContainer merged DRS config container
-     * @return merged server props
-     */
-    @Bean
-    public ServerProps getServerProps(
-        @Qualifier(DrsServerConstants.FINAL_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer drsConfigContainer
-    ) {
-        return drsConfigContainer.getDrs().getServerProps();
-    }
-
-    /**
-     * Retrieve database props object from merged DRS config container
-     * @param annotatedClasses list of hibernate entity classes to be managed by the DRS hibernate util
-     * @param drsConfigContainer merged DRS config container
-     * @return merged database props
-     */
-    @Bean
-    public DatabaseProps getDatabaseProps(
-        @Autowired List<Class<? extends HibernateEntity<? extends Serializable>>> annotatedClasses,
-        @Qualifier(DrsServerConstants.FINAL_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer drsConfigContainer
-    ) {
-        return drsConfigContainer.getDrs().getDatabaseProps();
-    }
-
-    /**
-     * Retrieve DRS service info object from merged DRS config container
-     * @param drsConfigContainer merged DRS config container
-     * @return merged DRS service info 
-     */
-    @Bean
-    public DrsServiceInfo getServiceInfo(
-        @Qualifier(DrsServerConstants.FINAL_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer drsConfigContainer
-    ) {
-        return drsConfigContainer.getDrs().getServiceInfo();
-    }
-
-    /**
-     * Retrieve DRS service properties from merged DRS config container
-     * @param drsConfigContainer merged DRS config container
-     * @return merged DRS service properties
-     */
-    @Bean
-    public DrsServiceProps getDrsServiceProps(
-        @Qualifier(DrsServerConstants.FINAL_DRS_CONFIG_CONTAINER) DrsServerYamlConfigContainer drsConfigContainer
-    ) {
-        return drsConfigContainer.getDrs().getDrsServiceProps();
-    }
-
-    /* ******************************
-     * LOGGING
-     * ****************************** */
-
-    @Bean
-    public LoggingUtil loggingUtil() {
-        return new LoggingUtil();
-    }
-
-    /* ******************************
-     * HIBERNATE CONFIG
-     * ****************************** */
-
-    /**
-     * List of hibernate entity classes to be managed by the Drs hibernate util
-     * @return list of DRS-related managed entity classes
-     */
-    @Bean
-    public List<Class<? extends HibernateEntity<? extends Serializable>>> getAnnotatedClasses() {
-        List<Class<? extends HibernateEntity<? extends Serializable>>> annotatedClasses = new ArrayList<>();
-        annotatedClasses.add(DrsObject.class);
-        annotatedClasses.add(Checksum.class);
-        annotatedClasses.add(FileAccessObject.class);
-        annotatedClasses.add(AwsS3AccessObject.class);
-        annotatedClasses.add(PassportBroker.class);
-        annotatedClasses.add(PassportVisa.class);
-        return annotatedClasses;
-    }
-
-    /**
-     * Loads/retrieves the hibernate util singleton providing access to DRS-related database tables
-     * @param annotatedClasses list of DRS-related entities to be managed
-     * @param databaseProps database properties from configuration
-     * @return loaded hibernate util singleton managing DRS entities
-     */
-    @Bean
-    public DrsHibernateUtil getDrsHibernateUtil(
-        @Autowired List<Class<? extends HibernateEntity<? extends Serializable>>> annotatedClasses,
-        @Autowired DatabaseProps databaseProps
-    ) {
-        DrsHibernateUtil hibernateUtil = new DrsHibernateUtil();
-        hibernateUtil.setAnnotatedClasses(annotatedClasses);
-        hibernateUtil.setDatabaseProps(databaseProps);
-        return hibernateUtil;
-    }
-
-    /* ******************************
-     * REQUEST HANDLER
-     * ****************************** */
-
-    /**
-     * Get new request handler facilitating access to a DRSObject
-     * @return drs object request handler
-     */
-    @Bean
-    @Scope(DrsServerConstants.PROTOTYPE)
-    public ObjectRequestHandler objectRequestHandler() {
-        return new ObjectRequestHandler();
-    }
-
-    /**
-     * Get new request handler facilitating the 'access' endpoint, i.e. provides
-     * an AccessURL for a given object_id and access_id
-     * @return access URL request handler
-     */
-    @Bean
-    @RequestScope
-    public AccessRequestHandler accessRequestHandler() {
-        return new AccessRequestHandler();
-    }
-
-        @Bean
-    @RequestScope
-    public AuthInfoRequestHandler authInfoRequestHandler() {
-        return new AuthInfoRequestHandler();
-    }
-
-    /**
-     * Get new request handler facilitating streaming of a local file over http(s)
-     * @return streaming request handler
-     */
-    @Bean
-    @RequestScope
-    public FileStreamRequestHandler fileStreamRequestHandler() {
-        return new FileStreamRequestHandler();
-    }
-
-    /* ******************************
-     * OTHER UTILS
-     * ****************************** */
-
-    /**
-     * Get cache singleton, storing object_id and access_id mappings
-     * @return object_id, access_id cache
-     */
-    @Bean
-    public AccessCache accessCache() {
-        return new AccessCache();
-    }
-
-    @Bean
-    public UserPassportMapVerifier userPAssportMapVerifier() {
-        return new UserPassportMapVerifier();
-    }
-}
diff --git a/deprecated/starterkit/drs/app/DrsServerYamlConfig.java b/deprecated/starterkit/drs/app/DrsServerYamlConfig.java
deleted file mode 100644
index 74b827b7..00000000
--- a/deprecated/starterkit/drs/app/DrsServerYamlConfig.java
+++ /dev/null
@@ -1,94 +0,0 @@
-package org.ga4gh.starterkit.drs.app;
-
-import org.ga4gh.starterkit.common.config.DatabaseProps;
-import org.ga4gh.starterkit.common.config.ServerProps;
-import org.ga4gh.starterkit.drs.config.DrsDatabaseProps;
-import org.ga4gh.starterkit.drs.config.DrsServiceProps;
-import org.ga4gh.starterkit.drs.model.DrsServiceInfo;
-
-/**
- * Contains multiple configuration objects affecting application behavior.
- * To be deserialized/loaded as part of a YAML config file specified on the 
- * command line
- */
-public class DrsServerYamlConfig {
-
-    private ServerProps serverProps;
-    private DrsDatabaseProps databaseProps;
-    private DrsServiceInfo serviceInfo;
-    private DrsServiceProps drsServiceProps;
-
-    /**
-     * Instantiates a new DrsStandaloneYamlConfig object with default properties
-     */
-    public DrsServerYamlConfig() {
-        serverProps = new ServerProps();
-        databaseProps = new DrsDatabaseProps();
-        serviceInfo = new DrsServiceInfo();
-        drsServiceProps = new DrsServiceProps();
-    }
-
-    /**
-     * Assign serverProps
-     * @param serverProps ServerProps object
-     */
-    public void setServerProps(ServerProps serverProps) {
-        this.serverProps = serverProps;
-    }
-
-    /**
-     * Retrieve server props
-     * @return ServerProps object
-     */
-    public ServerProps getServerProps() {
-        return serverProps;
-    }
-
-    /**
-     * Assign databaseProps
-     * @param databaseProps DatabaseProps object
-     */
-    public void setDatabaseProps(DrsDatabaseProps databaseProps) {
-        this.databaseProps = databaseProps;
-    }
-
-    /**
-     * Retrieve databaseProps
-     * @return DatabaseProps object
-     */
-    public DatabaseProps getDatabaseProps() {
-        return databaseProps;
-    }
-
-    /**
-     * Assign serviceInfo
-     * @param serviceInfo DrsServiceInfo object
-     */
-    public void setServiceInfo(DrsServiceInfo serviceInfo) {
-        this.serviceInfo = serviceInfo;
-    }
-
-    /**
-     * Retrieve serviceInfo
-     * @return DrsServiceInfo object
-     */
-    public DrsServiceInfo getServiceInfo() {
-        return serviceInfo;
-    }
-
-    /**
-     * Assign drsServiceProps
-     * @param drsServiceProps DrsServiceProps object
-     */
-    public void setDrsServiceProps(DrsServiceProps drsServiceProps) {
-        this.drsServiceProps = drsServiceProps;
-    }
-
-    /**
-     * Retrieve drsServiceProps
-     * @return DrsServiceProps object
-     */
-    public DrsServiceProps getDrsServiceProps() {
-        return drsServiceProps;
-    }
-}
diff --git a/deprecated/starterkit/drs/app/DrsServerYamlConfigContainer.java b/deprecated/starterkit/drs/app/DrsServerYamlConfigContainer.java
deleted file mode 100644
index 12c5c70f..00000000
--- a/deprecated/starterkit/drs/app/DrsServerYamlConfigContainer.java
+++ /dev/null
@@ -1,56 +0,0 @@
-package org.ga4gh.starterkit.drs.app;
-
-import org.ga4gh.starterkit.common.config.ContainsServerProps;
-import org.ga4gh.starterkit.common.config.ServerProps;
-
-/**
- * Top-level configuration container object for standalone deployments. To
- * be deserialized/loaded as part of a YAML config file specified on the command
- * line.
- */
-public class DrsServerYamlConfigContainer implements ContainsServerProps {
-
-    /**
-     * Nested configuration object
-     */
-    private DrsServerYamlConfig drs;
-
-    /**
-     * Instantiates a new DrsStandaloneYamlConfigContainer object with default properties
-     */
-    public DrsServerYamlConfigContainer() {
-        drs = new DrsServerYamlConfig();
-    }
-
-    /**
-     * Instantiates a new DrsStandaloneYamlConfigContainer with a preconfigured DrsStandaloneYamlConfig object
-     * @param drs preconfigured DrsStandaloneYamlConfig object
-     */
-    public DrsServerYamlConfigContainer(DrsServerYamlConfig drs) {
-        this.drs = drs;
-    }
-
-    /**
-     * Retrieve server props through the nested inner config object
-     * @return server props
-     */
-    public ServerProps getServerProps() {
-        return getDrs().getServerProps();
-    }
-
-    /**
-     * Assign drs
-     * @param drs DrsStandaloneYamlConfig object
-     */
-    public void setDrs(DrsServerYamlConfig drs) {
-        this.drs = drs;
-    }
-
-    /**
-     * Retrieve drs
-     * @return DrsStandaloneYamlConfig object
-     */
-    public DrsServerYamlConfig getDrs() {
-        return drs;
-    }
-}
diff --git a/deprecated/starterkit/drs/app/package-info.java b/deprecated/starterkit/drs/app/package-info.java
deleted file mode 100644
index 483de2b8..00000000
--- a/deprecated/starterkit/drs/app/package-info.java
+++ /dev/null
@@ -1,12 +0,0 @@
-/**
- * Enables running the Starter Kit DRS as a standalone web service
- * <p>
- * This package contains the classes necessary to deploy the Starter Kit DRS
- * as a standalone web service. Contains the main method, classes for loading
- * configurations, and Spring bean configuration
- * </p>
- * 
- * @since 0.1.4
- * @version 0.1.4
- */
-package org.ga4gh.starterkit.drs.app;
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/config/DatabaseType.java b/deprecated/starterkit/drs/config/DatabaseType.java
deleted file mode 100644
index 792722e4..00000000
--- a/deprecated/starterkit/drs/config/DatabaseType.java
+++ /dev/null
@@ -1,10 +0,0 @@
-package org.ga4gh.starterkit.drs.config;
-
-/**
- * @author dashrath
- */
-public enum DatabaseType {
-    mysql,
-    postgres,
-    sqlite
-}
diff --git a/deprecated/starterkit/drs/config/DrsDatabaseProps.java b/deprecated/starterkit/drs/config/DrsDatabaseProps.java
deleted file mode 100644
index ad13ca36..00000000
--- a/deprecated/starterkit/drs/config/DrsDatabaseProps.java
+++ /dev/null
@@ -1,97 +0,0 @@
-package org.ga4gh.starterkit.drs.config;
-
-import org.ga4gh.starterkit.common.config.DatabaseProps;
-
-import java.util.Properties;
-
-import static org.ga4gh.starterkit.common.constant.DatabasePropsConstants.*;
-
-/**
- * @author dashrath
- */
-public class DrsDatabaseProps extends DatabaseProps {
-
-    private String url;
-    private String username;
-    private String password;
-    private String poolSize;
-    private String showSQL;
-
-    // constants for mysql db type
-    public static final String MYSQL_DRIVER_CLASS = "com.mysql.cj.jdbc.Driver";
-    public static final String MYSQL_DIALECT = "org.hibernate.dialect.MySQL8Dialect";
-
-    public Properties getAllProperties() {
-        Properties props = new Properties();
-
-        // set common properties across any db type: url, username, password,
-        // pool_size, show_sql,
-        props.setProperty("hibernate.connection.url", getUrl());
-
-        if (!getUsername().equals("")) {
-            props.setProperty("hibernate.connection.username", getUsername());
-        }
-
-        if (!getPassword().equals("")) {
-            props.setProperty("hibernate.connection.password", getPassword());
-        }
-
-        props.setProperty("hibernate.connection.pool_size", getPoolSize());
-        props.setProperty("hibernate.show_sql", getShowSQL());
-
-        // set hardcoded properties: current_session_context_class
-        props.setProperty("hibernate.current_session_context_class", DEFAULT_CURRENT_SESSION_CONTEXT_CLASS);
-
-        // infer database type (ie sqlite or postgresql) from the db connection url
-        DatabaseType dbtype = getDatabaseTypeFromUrl(getUrl());
-
-        switch(dbtype) {
-            case mysql:
-                assignMySQLProperties(props);
-                break;
-
-            case postgres:
-                assignPostgresProperties(props);
-                break;
-
-            case sqlite:
-                assignSqliteProperties(props);
-                break;
-        }
-
-        return props;
-    }
-
-    private DatabaseType getDatabaseTypeFromUrl(String url) {
-
-        if (url.startsWith("jdbc:sqlite")) {
-            return DatabaseType.sqlite;
-        }
-
-        if (url.startsWith("jdbc:postgresql")) {
-            return DatabaseType.postgres;
-        }
-
-        if (url.startsWith("jdbc:mysql")) {
-            return DatabaseType.mysql;
-        }
-
-        throw new IllegalArgumentException("Invalid JDBC URL: MUST be a valid 'sqlite', 'postgresql', or 'mysql' JDBC URL");
-    }
-
-    private void assignSqliteProperties(Properties props) {
-        props.setProperty("hibernate.connection.driver_class", SQLITE_DRIVER_CLASS);
-        props.setProperty("hibernate.dialect", SQLITE_DIALECT);
-        props.setProperty("hibernate.connection.date_class", SQLITE_DATE_CLASS);
-    }
-
-    private void assignPostgresProperties(Properties props) {
-        props.setProperty("hibernate.connection.driver_class", POSTGRES_DRIVER_CLASS);
-        props.setProperty("hibernate.dialect", POSTGRES_DIALECT);
-    }
-
-    private void assignMySQLProperties(Properties props) {
-        props.setProperty("hibernate.connection.driver_class", MYSQL_DRIVER_CLASS);
-        props.setProperty("hibernate.dialect", MYSQL_DIALECT);
-    }
-}
diff --git a/deprecated/starterkit/drs/config/DrsServiceProps.java b/deprecated/starterkit/drs/config/DrsServiceProps.java
deleted file mode 100644
index 060a034c..00000000
--- a/deprecated/starterkit/drs/config/DrsServiceProps.java
+++ /dev/null
@@ -1,71 +0,0 @@
-package org.ga4gh.starterkit.drs.config;
-
-/**
- * Configuration properties modifying application behaviour that are unique
- * only to DRS. To be deserialized/loaded from YAML config file
- */
-public class DrsServiceProps {
-
-    /**
-     * Indicates whether the DRS service should provide file URLs of DRSObject
-     * file location back to the client. If true, assumes that client has 
-     * access to the same filesystem as the service (e.g. HPC environment).
-     * Applies only to 'file' based objects (ie not https, s3, etc.)
-     */
-    private boolean serveFileURLForFileObjects;
-
-    /**
-     * Indicates whether the DRS service should provide the streaming endpoint
-     * URL to the client, for files that the server can access but the client
-     * cannot. If true, assumes that client cannot access the file by its path.
-     * Applies only to 'file' based objects (ie not https, s3, etc.)
-     */
-    private boolean serveStreamURLForFileObjects;
-
-    /**
-     * Instantiates a new DrsServiceProps object with all defaults
-     */
-    public DrsServiceProps() {
-        setAllDefaults();
-    }
-
-    /**
-     * Assign boolean, indicating whether to serve file paths
-     * @param serveFileURLForFileObjects boolean indicator
-     */
-    public void setServeFileURLForFileObjects(boolean serveFileURLForFileObjects) {
-        this.serveFileURLForFileObjects = serveFileURLForFileObjects;
-    }
-
-    /**
-     * Retrieve boolean indicating whether to serve file paths
-     * @return boolean indicator
-     */
-    public boolean getServeFileURLForFileObjects() {
-        return serveFileURLForFileObjects;
-    }
-
-    /**
-     * Assign boolean, indicating whether to serve files via stream endpoint
-     * @param serveStreamURLForFileObjects boolean indicator
-     */
-    public void setServeStreamURLForFileObjects(boolean serveStreamURLForFileObjects) {
-        this.serveStreamURLForFileObjects = serveStreamURLForFileObjects;
-    }
-
-    /**
-     * Retrieve boolean, indicating whether to serve files via stream endpoint
-     * @return boolean indicator
-     */
-    public boolean getServeStreamURLForFileObjects() {
-        return serveStreamURLForFileObjects;
-    }
-
-    /**
-     * Initialize DRS service props with defaults
-     */
-    private void setAllDefaults() {
-        serveFileURLForFileObjects = true;
-        serveStreamURLForFileObjects = false;
-    }
-}
diff --git a/deprecated/starterkit/drs/config/package-info.java b/deprecated/starterkit/drs/config/package-info.java
deleted file mode 100644
index 6f50f760..00000000
--- a/deprecated/starterkit/drs/config/package-info.java
+++ /dev/null
@@ -1,8 +0,0 @@
-/**
- * Defines configuration classes modifying application behavior that are unique
- * only to DRS. Generally deserialized/loaded from YAML config file
- * 
- * @since 0.1.4
- * @version 0.1.4
- */
-package org.ga4gh.starterkit.drs.config;
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/constant/DrsApiConstants.java b/deprecated/starterkit/drs/constant/DrsApiConstants.java
deleted file mode 100644
index 187fe678..00000000
--- a/deprecated/starterkit/drs/constant/DrsApiConstants.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.ga4gh.starterkit.drs.constant;
-
-import static org.ga4gh.starterkit.common.constant.StarterKitConstants.ADMIN;
-import static org.ga4gh.starterkit.common.constant.StarterKitConstants.GA4GH;
-import static org.ga4gh.starterkit.common.constant.StarterKitConstants.DRS;
-import static org.ga4gh.starterkit.common.constant.StarterKitConstants.V1;
-
-/**
- * DRS API URL path/routing constants
- */
-public class DrsApiConstants {
-
-    /**
-     * Common REST API route to most (if not all) DRS-related controller functions
-     */
-    public static final String DRS_API_V1 = "/" + GA4GH + "/" + DRS + "/" + V1;
-
-    /**
-     * Common REST API route to most (if not all) off-spec, administrative controller
-     * functions for modifying DRS-related entities
-     */
-    public static final String ADMIN_DRS_API_V1 = "/" + ADMIN + DRS_API_V1;
-}
diff --git a/deprecated/starterkit/drs/constant/DrsServiceInfoDefaults.java b/deprecated/starterkit/drs/constant/DrsServiceInfoDefaults.java
deleted file mode 100644
index a5b7315a..00000000
--- a/deprecated/starterkit/drs/constant/DrsServiceInfoDefaults.java
+++ /dev/null
@@ -1,83 +0,0 @@
-package org.ga4gh.starterkit.drs.constant;
-
-import java.time.LocalDateTime;
-
-import org.ga4gh.starterkit.common.constant.DateTimeConstants;
-
-/**
- * Default values for the DRS service info response
- */
-public class DrsServiceInfoDefaults {
-
-    /**
-     * Default service id
-     */
-    public static final String ID = "org.ga4gh.starterkit.drs";
-
-    /**
-     * Default service name
-     */
-    public static final String NAME = "GA4GH Starter Kit DRS Service";
-
-    /**
-     * Default service description
-     */
-    public static final String DESCRIPTION = "An open source, community-driven"
-        + " implementation of the GA4GH Data Repository Service (DRS)"
-        + " API specification.";
-
-    /**
-     * Default service contact URL
-     */
-    public static final String CONTACT_URL = "mailto:info@ga4gh.org";
-
-    /**
-     * Default service documentation URL
-     */
-    public static final String DOCUMENTATION_URL = "https://github.com/ga4gh/ga4gh-starter-kit-drs";
-
-    /**
-     * Default service creation/launch time
-     */
-    public static final LocalDateTime CREATED_AT = LocalDateTime.parse("2020-01-15T12:00:00Z", DateTimeConstants.DATE_FORMATTER);
-
-    /**
-     * Default service last updated time
-     */
-    public static final LocalDateTime UPDATED_AT = LocalDateTime.parse("2020-01-15T12:00:00Z", DateTimeConstants.DATE_FORMATTER);;
-
-    /**
-     * Default service environment
-     */
-    public static final String ENVIRONMENT = "test";
-
-    /**
-     * Default service version
-     */
-    public static final String VERSION = "0.3.2";
-
-    /**
-     * Default service organization name
-     */
-    public static final String ORGANIZATION_NAME = "Global Alliance for Genomics and Health";
-
-    /**
-     * Default service organization URL
-     */
-    public static final String ORGANIZATION_URL = "https://ga4gh.org";
-
-    /**
-     * Default service type group
-     */
-    public static final String SERVICE_TYPE_GROUP = "org.ga4gh";
-
-    /**
-     * Default service type artifact
-     */
-    public static final String SERVICE_TYPE_ARTIFACT = "drs";
-
-    /**
-     * Default service type version
-     */
-    public static final String SERVICE_TYPE_VERSION = "1.3.0experimental";
-}
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/constant/package-info.java b/deprecated/starterkit/drs/constant/package-info.java
deleted file mode 100644
index 56bdac2f..00000000
--- a/deprecated/starterkit/drs/constant/package-info.java
+++ /dev/null
@@ -1,7 +0,0 @@
-/**
- * Contains program-wide constants to be used by various components of the DRS API
- * 
- * @since 0.1.4
- * @version 0.1.4
- */
-package org.ga4gh.starterkit.drs.constant;
diff --git a/deprecated/starterkit/drs/controller/DrsAdmin.java b/deprecated/starterkit/drs/controller/DrsAdmin.java
deleted file mode 100644
index 17ff1c83..00000000
--- a/deprecated/starterkit/drs/controller/DrsAdmin.java
+++ /dev/null
@@ -1,206 +0,0 @@
-package org.ga4gh.starterkit.drs.controller;
-
-import com.fasterxml.jackson.annotation.JsonView;
-import org.ga4gh.starterkit.common.exception.BadRequestException;
-import org.ga4gh.starterkit.common.exception.ConflictException;
-import org.ga4gh.starterkit.common.exception.ResourceNotFoundException;
-import org.ga4gh.starterkit.common.hibernate.exception.EntityDoesntExistException;
-import org.ga4gh.starterkit.common.hibernate.exception.EntityExistsException;
-import org.ga4gh.starterkit.common.hibernate.exception.EntityMismatchException;
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
-import org.ga4gh.starterkit.drs.model.DrsObject;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.ga4gh.starterkit.drs.utils.hibernate.DrsHibernateUtil;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.MediaType;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.*;
-import org.springframework.web.multipart.MultipartFile;
-
-import java.util.List;
-
-import static org.ga4gh.starterkit.drs.constant.DrsApiConstants.ADMIN_DRS_API_V1;
-
-/**
- * Controller functions for the administrative API, create and modify DRS-related
- * entities
- */
-@RestController
-@RequestMapping(ADMIN_DRS_API_V1 + "/objects") // /admin/ga4gh/drs/v1
-public class DrsAdmin {
-
-    @Autowired
-    private DrsHibernateUtil hibernateUtil;
-
-    @Autowired
-    private LoggingUtil loggingUtil;
-
-    // Non-standard endpoints - admin views
-
-    /**
-     * Display DRSObject list
-     * @return DRSObject list
-     */
-    @GetMapping
-    @JsonView(SerializeView.Always.class)
-    public List<DrsObject> indexDrsObjects() {
-        loggingUtil.debug("Admin API request: DrsObject list");
-        return hibernateUtil.getEntityList(DrsObject.class);
-    }
-
-    /**
-     * Display all data for a single DRSObject
-     * @param id identifier for DRSObject of interest
-     * @return metadata for DRSObject
-     */
-    @GetMapping(path = "/{object_id:.+}")
-    @JsonView(SerializeView.Admin.class)
-    public DrsObject showDrsObject(
-        @PathVariable(name = "object_id") String id
-    ) {
-        loggingUtil.debug("Admin API request: DrsObject with id '" + id + "'");
-        DrsObject drsObject = hibernateUtil.loadDrsObject(id, false);
-        if (drsObject == null) {
-            String exceptionMessage = "No DrsObject found by id: " + id;
-            loggingUtil.error("Exception occurred: " + exceptionMessage);
-            throw new ResourceNotFoundException(exceptionMessage);
-        }
-        return getAdminFormattedDrsObject(id);
-    }
-
-    // Non-standard endpoints - write operations
-
-    /**
-     * Create a new DRSObject in the database
-     * @param drsObject new, non persistent DRSObject
-     * @return persistent DRSObject saved with the requested attributes
-     */
-    @PostMapping(consumes = MediaType.APPLICATION_JSON_VALUE)
-    @JsonView(SerializeView.Admin.class)
-    public DrsObject createDrsObject(
-        @RequestBody DrsObject drsObject
-    ) {
-        loggingUtil.debug("Admin API request: create new DrsObject");
-        loggingUtil.trace(drsObject.toString());
-        try {
-            hibernateUtil.createEntityObject(DrsObject.class, drsObject);
-            return getAdminFormattedDrsObject(drsObject.getId());
-        } catch (EntityExistsException ex) {
-            loggingUtil.error("Exception occurred: Entity exists exception" + ex.getMessage());
-            throw new ConflictException(ex.getMessage());
-        }
-    }
-
-    /**
-     * Update an existing DRSObject with new properties
-     * @param id identifier of DRSObject to be modified
-     * @param drsObject new DRSObject properties
-     * @return persistent DRSObject with overwritten attributes according to request body
-     */
-    @PutMapping(path = "/{object_id:.+}")
-    public DrsObject updateDrsObject(
-        @PathVariable(name = "object_id") String id,
-        @RequestBody DrsObject drsObject
-    ) {
-        loggingUtil.debug("Admin API request: update DrsObject with id '" + id + "'");
-        loggingUtil.trace(drsObject.toString());
-        try {
-            hibernateUtil.updateEntityObject(DrsObject.class, id, drsObject);
-            return getAdminFormattedDrsObject(id);
-        } catch (EntityMismatchException ex) {
-            loggingUtil.error("Exception occurred: Entity mismatch exception" + ex.getMessage());
-            throw new BadRequestException(ex.getMessage());
-        } catch (EntityDoesntExistException ex) {
-            loggingUtil.error("Exception occurred: Entity mismatch exception" + ex.getMessage());
-            throw new ConflictException(ex.getMessage());
-        }
-    }
-
-    /**
-     * Delete an existing DRSObject
-     * @param id identifier of DRSObject to be deleted
-     * @return empty response body, indicating successful deletion
-     */
-    @DeleteMapping(path = "/{object_id:.+}")
-    public DrsObject deleteDrsObject(
-        @PathVariable(name = "object_id") String id
-    ) {
-        loggingUtil.debug("Admin API request: delete DrsObject with id '" + id + "'");
-        try {
-            hibernateUtil.deleteEntityObject(DrsObject.class, id);
-            return hibernateUtil.readEntityObject(DrsObject.class, id, false);
-        } catch (EntityDoesntExistException ex) {
-            loggingUtil.error("Exception occurred: entity doesnt exist exception" + ex.getMessage());
-            throw new ConflictException(ex.getMessage());
-        } catch (EntityExistsException ex) {
-            loggingUtil.error("Exception occurred: entity exists exception" + ex.getMessage());
-            throw new ConflictException(ex.getMessage());
-        }
-    }
-
-    /**
-     * High-level function to load a DRSObject with all necessary properties
-     * to get an administrative view, while avoiding infinite recursive 
-     * deserialization problem
-     * @param id identifier of DRSObject to be loaded
-     * @return administrative view of DRSObject
-     */
-    private DrsObject getAdminFormattedDrsObject(String id) {
-        DrsObject drsObject = hibernateUtil.loadDrsObject(id, false);
-        breakInterminableFetchForChildrenAndParents(drsObject);
-        return drsObject;
-    }
-
-    /**
-     * For a given DRSObject, avoid infinite recursive serialization by setting
-     * certain attributes of its parents and children to null
-     * @param drsObject DRSObject to be loaded
-     */
-    private void breakInterminableFetchForChildrenAndParents(DrsObject drsObject) {
-        for (DrsObject childDrsObject: drsObject.getDrsObjectChildren()) {
-            // each of the DRSObject's children have certain attributes set to
-            // null to avoid infinite serialization
-            breakInterminableFetch(childDrsObject);
-        }
-        for (DrsObject parentDrsObject: drsObject.getDrsObjectParents()) {
-            // each of the DRSObject's parents have certain attributes set to
-            // null to avoid infinite serialization
-            breakInterminableFetch(parentDrsObject);
-        }
-    }
-
-    /**
-     * Assign certain attributes to null to avoid infinite recursive serialization.
-     * Only for administrative views of an object, does not affect the persistent
-     * state of an object
-     * @param drsObject DRSObject to be modified
-     */
-    private void breakInterminableFetch(DrsObject drsObject) {
-        drsObject.setAliases(null);
-        drsObject.setChecksums(null);
-        drsObject.setFileAccessObjects(null);
-        drsObject.setAwsS3AccessObjects(null);
-        drsObject.setDrsObjectChildren(null);
-        drsObject.setDrsObjectParents(null);
-        drsObject.setPassportVisas(null);
-    }
-
-    /**
-     * Loads multiple DRS Objects into database
-     * @param file
-     * @return persistent DRSObject saved with the requested attributes
-     */
-    @PostMapping(path = "/bulkInsert")
-    @JsonView(SerializeView.Admin.class)
-    public ResponseEntity<String> bulkInsert(@RequestParam("file") MultipartFile file) {
-        loggingUtil.debug("Admin API request: bulk insert DRS objects");
-        try {
-            hibernateUtil.insertBulkDrsObjects(file);
-            return new ResponseEntity<>("File uploaded and data inserted successfully", HttpStatus.OK);
-        } catch (Exception e) {
-            loggingUtil.error("Error processing the file: " + e.getMessage()+ e);
-            return new ResponseEntity<>("Error processing the file: " + e.getMessage(), HttpStatus.INTERNAL_SERVER_ERROR);
-        }
-    }
-}
diff --git a/deprecated/starterkit/drs/controller/DrsServiceInfo.java b/deprecated/starterkit/drs/controller/DrsServiceInfo.java
deleted file mode 100644
index 736736e3..00000000
--- a/deprecated/starterkit/drs/controller/DrsServiceInfo.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package org.ga4gh.starterkit.drs.controller;
-
-import static org.ga4gh.starterkit.drs.constant.DrsApiConstants.DRS_API_V1;
-
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.RestController;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * Service info controller, displays generic and DRS-specific service info
- */
-@RestController
-@RequestMapping(DRS_API_V1 + "/service-info")
-public class DrsServiceInfo {
-
-    @Autowired
-    private org.ga4gh.starterkit.drs.model.DrsServiceInfo drsServiceInfo;
-
-    @Autowired
-    private LoggingUtil loggingUtil;
-
-    /**
-     * Display service info
-     * @return DRS service info
-     */
-    @GetMapping //(produces = MediaType.APPLICATION_JSON_VALUE)
-    public org.ga4gh.starterkit.drs.model.DrsServiceInfo getServiceInfo() {
-        loggingUtil.debug("Public API request: service info");
-        loggingUtil.trace(drsServiceInfo.toString());
-        return drsServiceInfo;
-    }
-}
diff --git a/deprecated/starterkit/drs/controller/Objects.java b/deprecated/starterkit/drs/controller/Objects.java
deleted file mode 100644
index 1063420b..00000000
--- a/deprecated/starterkit/drs/controller/Objects.java
+++ /dev/null
@@ -1,207 +0,0 @@
-package org.ga4gh.starterkit.drs.controller;
-
-import static org.ga4gh.starterkit.drs.constant.DrsApiConstants.DRS_API_V1;
-
-import java.util.ArrayList;
-import java.util.List;
-import org.ga4gh.starterkit.common.exception.CustomException;
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
-import org.ga4gh.starterkit.drs.model.AccessURL;
-import org.ga4gh.starterkit.drs.model.AuthInfo;
-import org.ga4gh.starterkit.drs.model.BulkAccessRequest;
-import org.ga4gh.starterkit.drs.model.BulkAuthInfoRequest;
-import org.ga4gh.starterkit.drs.model.BulkAuthInfoResponse;
-import org.ga4gh.starterkit.drs.model.BulkObjectAccessId;
-import org.ga4gh.starterkit.drs.model.BulkRequest;
-import org.ga4gh.starterkit.drs.model.BulkResponse;
-import org.ga4gh.starterkit.drs.model.DrsObject;
-import org.ga4gh.starterkit.drs.model.PostSingleObjectRequestBody;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.ga4gh.starterkit.drs.utils.passport.UserPassportMap;
-import org.ga4gh.starterkit.drs.utils.passport.UserPassportMapVerifier;
-import org.ga4gh.starterkit.drs.utils.requesthandler.AccessRequestHandler;
-import org.ga4gh.starterkit.drs.utils.requesthandler.AuthInfoRequestHandler;
-import org.ga4gh.starterkit.drs.utils.requesthandler.ObjectRequestHandler;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.ApplicationContext;
-import org.springframework.context.ApplicationContextAware;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.PostMapping;
-import org.springframework.web.bind.annotation.RequestBody;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RequestMethod;
-import org.springframework.web.bind.annotation.RestController;
-import org.springframework.web.bind.annotation.RequestParam;
-import org.springframework.web.bind.annotation.ResponseStatus;
-import javax.annotation.Resource;
-import com.fasterxml.jackson.annotation.JsonView;
-
-/**
- * Controller functions for accessing DRSObjects according to the DRS specification
- */
-@RestController
-@RequestMapping(DRS_API_V1 + "/objects")
-public class Objects implements ApplicationContextAware {
-
-    @Resource(name = "objectRequestHandler")
-    private ObjectRequestHandler objectRequestHandler;
-
-    @Resource(name = "accessRequestHandler")
-    private AccessRequestHandler accessRequestHandler;
-
-    @Resource(name = "authInfoRequestHandler")
-    private AuthInfoRequestHandler authInfoRequestHandler;
-
-    @Autowired
-    private LoggingUtil loggingUtil;
-
-    @Autowired
-    private UserPassportMapVerifier passportVerifier;
-
-    private ApplicationContext context;
-
-    // Standard endpoints
-
-    /**
-     * Show information about a DRS object
-     * @param objectId identifier of DRSObject of interest 
-     * @param expand if true, display recursive bundling under 'contents' property
-     * @return DRSObject by the requested id
-     */
-    @GetMapping(path = "/{object_id:.+}")
-    @JsonView(SerializeView.Public.class)
-    public DrsObject getObjectById(
-        @PathVariable(name = "object_id") String objectId,
-        @RequestParam(name = "expand", required = false) boolean expand
-    ) {
-        loggingUtil.debug("Public API request: DrsObject with id '" + objectId + "', expand=" + expand);
-        return objectRequestHandler.prepare(objectId, expand, null).handleRequest();
-    }
-
-    @PostMapping(path = "/{object_id:.+}")
-    @JsonView(SerializeView.Public.class)
-    public DrsObject getObjectByIdViaPost(
-        @PathVariable(name = "object_id") String objectId,
-        @RequestBody PostSingleObjectRequestBody requestBody
-    ) {
-        UserPassportMap userPassportMap = null;
-        if (requestBody.getPassports() != null) {
-            userPassportMap = new UserPassportMap(requestBody.getPassports());
-            passportVerifier.verifyAll(userPassportMap);
-        }
-        return objectRequestHandler.prepare(objectId, requestBody.isExpand(), userPassportMap).handleRequest();
-    }
-
-    @RequestMapping(value = "/{object_id:.+}", method = RequestMethod.OPTIONS)
-    @JsonView(SerializeView.Public.class)
-    public AuthInfo singleObjectAuthInfo(
-        @PathVariable(name = "object_id") String objectId
-    ) {
-        return authInfoRequestHandler.prepare(objectId).handleRequest();
-    }
-
-    /**
-     * Get an access URL for fetching the DRS Object's  file bytes
-     * @param objectId DRSObject identifier
-     * @param accessId access identifier
-     * @return a DRS-spec AccessURL indicating file bytes location
-     */
-    @GetMapping(path = "/{object_id:.+}/access/{access_id:.+}")
-    public AccessURL getAccessURLById(
-        @PathVariable(name = "object_id") String objectId,
-        @PathVariable(name = "access_id") String accessId
-    ) {
-        loggingUtil.debug("Public API request: AccessURL for DRS id '" + objectId + "', access id '" + accessId + "'");
-        return accessRequestHandler.prepare(objectId, accessId).handleRequest();
-    }
-
-    @PostMapping
-    @JsonView(SerializeView.Public.class)
-    public BulkResponse getBulkObjects(
-        @RequestBody BulkRequest bulkRequest
-    ) {
-        // parse user passport
-        UserPassportMap userPassportMap = null;
-        if (bulkRequest.getPassports() != null) {
-            userPassportMap = new UserPassportMap(bulkRequest.getPassports());
-            passportVerifier.verifyAll(userPassportMap);
-        }
-
-        BulkResponse bulkResponse = new BulkResponse();
-        int requested = 0;
-        int resolved = 0;
-        int unresolved = 0;
-
-        for (String drsObjectId : bulkRequest.getSelection()) {
-            requested++;
-            try {
-                ObjectRequestHandler handler = context.getBean(ObjectRequestHandler.class);
-                DrsObject drsObject = handler.prepare(drsObjectId, false, userPassportMap).handleRequest();
-                bulkResponse.getResolvedDrsObject().add(drsObject);
-                resolved++;
-            } catch (CustomException ex) {
-                int httpStatus = ex.getClass().getAnnotation(ResponseStatus.class).value().value();
-                bulkResponse.getUnresolvedDrsObject().put(drsObjectId, httpStatus);
-                unresolved++;
-            }
-        }
-        bulkResponse.getSummary().setRequested(requested);
-        bulkResponse.getSummary().setResolved(resolved);
-        bulkResponse.getSummary().setUnresolved(unresolved);
-
-        return bulkResponse;
-    }
-
-    @RequestMapping(method = RequestMethod.OPTIONS)
-    @JsonView(SerializeView.Public.class)
-    public BulkAuthInfoResponse getBulkAuthInfo(
-        @RequestBody BulkAuthInfoRequest request
-    ) {
-        BulkAuthInfoResponse response = new BulkAuthInfoResponse();
-        int requested = 0;
-        int resolved = 0;
-        int unresolved = 0;
-
-        for (String drsObjectId : request.getSelection()) {
-            requested++;
-            try {
-                AuthInfoRequestHandler handler = context.getBean(AuthInfoRequestHandler.class);
-                AuthInfo authInfo = handler.prepare(drsObjectId).handleRequest();
-                response.getResolvedDrsObjectAuthInfo().put(drsObjectId, authInfo);
-                resolved++;
-            } catch (CustomException ex) {
-                int httpStatus = ex.getClass().getAnnotation(ResponseStatus.class).value().value();
-                response.getUnresolvedDrsObjectAuthInfo().put(drsObjectId, httpStatus);
-                unresolved++;
-            }
-        }
-        response.getSummary().setRequested(requested);
-        response.getSummary().setResolved(resolved);
-        response.getSummary().setUnresolved(unresolved);
-        return response;
-    }
-
-    @PostMapping(path = "/access")
-    @JsonView(SerializeView.Public.class)
-    public List<AccessURL> getBulkAccessURLs(
-        @RequestBody BulkAccessRequest bulkAccessRequest
-    ) {
-        List<AccessURL> accessURLs = new ArrayList<>();
-        for (BulkObjectAccessId idPair : bulkAccessRequest.getSelection()) {
-            try {
-                AccessRequestHandler handler = context.getBean(AccessRequestHandler.class);
-                AccessURL accessURL = handler.prepare(idPair.getObjectId(), idPair.getAccessId()).handleRequest();
-                accessURLs.add(accessURL);
-            } catch (CustomException ex) {
-                loggingUtil.error("Exception occurred: " + ex.getMessage());
-            }
-        }
-
-        return accessURLs;
-    }
-
-    public void setApplicationContext(ApplicationContext context) {
-        this.context = context;
-    }
-}
diff --git a/deprecated/starterkit/drs/controller/Stream.java b/deprecated/starterkit/drs/controller/Stream.java
deleted file mode 100644
index 4fae8209..00000000
--- a/deprecated/starterkit/drs/controller/Stream.java
+++ /dev/null
@@ -1,43 +0,0 @@
-package org.ga4gh.starterkit.drs.controller;
-
-import javax.annotation.Resource;
-import javax.servlet.http.HttpServletResponse;
-import static org.ga4gh.starterkit.drs.constant.DrsApiConstants.DRS_API_V1;
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
-import org.ga4gh.starterkit.drs.utils.requesthandler.FileStreamRequestHandler;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.web.bind.annotation.GetMapping;
-import org.springframework.web.bind.annotation.PathVariable;
-import org.springframework.web.bind.annotation.RequestMapping;
-import org.springframework.web.bind.annotation.RestController;
-
-/**
- * Stream handler, enables client to access bytes for files on the server machine
- * that the client doesn't have direct access to 
- */
-@RestController
-@RequestMapping(DRS_API_V1 + "/stream")
-public class Stream {
-
-    @Resource(name = "fileStreamRequestHandler")
-    private FileStreamRequestHandler fileStreamRequestHandler;
-
-    @Autowired
-    private LoggingUtil loggingUtil;
-
-    /**
-     * Stream file bytes for the requested DRSObject and access id
-     * @param objectId DRSObject identifier
-     * @param accessId access identifier
-     * @param response Spring HttpServletResponse
-     */
-    @GetMapping(path = "/{object_id:.+}/{access_id:.+}")
-    public void streamFile(
-        @PathVariable(name = "object_id") String objectId,
-        @PathVariable(name = "access_id") String accessId,
-        HttpServletResponse response
-    ) {
-        loggingUtil.debug("Public API request: local file streaming. drs id='" + objectId + "', access id='" + accessId + "'");
-        fileStreamRequestHandler.prepare(objectId, accessId, response).handleRequest();
-    }
-}
diff --git a/deprecated/starterkit/drs/controller/package-info.java b/deprecated/starterkit/drs/controller/package-info.java
deleted file mode 100644
index f8213cbb..00000000
--- a/deprecated/starterkit/drs/controller/package-info.java
+++ /dev/null
@@ -1,4 +0,0 @@
-/**
- * Contains REST API controller functions
- */
-package org.ga4gh.starterkit.drs.controller;
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/exception/DrsCustomExceptionHandling.java b/deprecated/starterkit/drs/exception/DrsCustomExceptionHandling.java
deleted file mode 100644
index fb6b9cfd..00000000
--- a/deprecated/starterkit/drs/exception/DrsCustomExceptionHandling.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package org.ga4gh.starterkit.drs.exception;
-
-import java.time.LocalDateTime;
-
-import org.ga4gh.starterkit.common.constant.DateTimeConstants;
-import org.ga4gh.starterkit.common.exception.CustomException;
-import org.ga4gh.starterkit.common.util.webserver.CustomExceptionHandling;
-import org.springframework.http.HttpStatus;
-import org.springframework.http.ResponseEntity;
-import org.springframework.web.bind.annotation.ExceptionHandler;
-import org.springframework.web.bind.annotation.ResponseStatus;
-
-public class DrsCustomExceptionHandling extends CustomExceptionHandling {
-
-    @ExceptionHandler(CustomException.class)
-    public ResponseEntity<Object> handleCustomExceptions(CustomException err) {
-        HttpStatus httpStatus = getCustomHttpStatus(err);
-        return yieldResponseEntity(httpStatus, err);
-    }
-
-    private HttpStatus getCustomHttpStatus(CustomException err) {
-        return err.getClass().getAnnotation(ResponseStatus.class).value();
-    }
-
-    private ResponseEntity<Object> yieldResponseEntity(HttpStatus httpStatus, Exception ex) {
-        DrsCustomExceptionResponse response = new DrsCustomExceptionResponse();
-        response.setTimestamp(LocalDateTime.now().format(DateTimeConstants.DATE_FORMATTER));
-        response.setStatusCode(httpStatus.value());
-        response.setError(httpStatus.getReasonPhrase());
-        response.setMsg(ex.getMessage());
-        return new ResponseEntity<>(response, httpStatus);
-    }
-}
diff --git a/deprecated/starterkit/drs/exception/DrsCustomExceptionResponse.java b/deprecated/starterkit/drs/exception/DrsCustomExceptionResponse.java
deleted file mode 100644
index 70bb68e1..00000000
--- a/deprecated/starterkit/drs/exception/DrsCustomExceptionResponse.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package org.ga4gh.starterkit.drs.exception;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.common.exception.CustomExceptionResponse;
-
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-public class DrsCustomExceptionResponse extends CustomExceptionResponse {
-
-    private String msg;
-
-    public void setMsg(String msg) {
-        this.msg = msg;
-    }
-
-    public String getMsg() {
-        return msg;
-    }
-}
diff --git a/deprecated/starterkit/drs/exception/ForbiddenException.java b/deprecated/starterkit/drs/exception/ForbiddenException.java
deleted file mode 100644
index ab6185b2..00000000
--- a/deprecated/starterkit/drs/exception/ForbiddenException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.ga4gh.starterkit.drs.exception;
-
-import org.ga4gh.starterkit.common.exception.CustomException;
-import org.springframework.http.HttpStatus;
-import org.springframework.web.bind.annotation.ResponseStatus;
-
-@ResponseStatus(value = HttpStatus.FORBIDDEN)
-public class ForbiddenException extends CustomException {
-
-    private static final long serialVersionUID = 1L;
-
-    public ForbiddenException() {
-        super();
-    }
-
-    public ForbiddenException(String message) {
-        super(message);
-    }
-
-    public ForbiddenException(Throwable cause) {
-        super(cause);
-    }
-}
diff --git a/deprecated/starterkit/drs/exception/UnauthorizedException.java b/deprecated/starterkit/drs/exception/UnauthorizedException.java
deleted file mode 100644
index 6c624308..00000000
--- a/deprecated/starterkit/drs/exception/UnauthorizedException.java
+++ /dev/null
@@ -1,23 +0,0 @@
-package org.ga4gh.starterkit.drs.exception;
-
-import org.ga4gh.starterkit.common.exception.CustomException;
-import org.springframework.http.HttpStatus;
-import org.springframework.web.bind.annotation.ResponseStatus;
-
-@ResponseStatus(value = HttpStatus.UNAUTHORIZED)
-public class UnauthorizedException extends CustomException {
-
-    private static final long serialVersionUID = 1L;
-
-    public UnauthorizedException() {
-        super();
-    }
-
-    public UnauthorizedException(String message) {
-        super(message);
-    }
-
-    public UnauthorizedException(Throwable cause) {
-        super(cause);
-    }
-}
diff --git a/deprecated/starterkit/drs/model/AccessMethod.java b/deprecated/starterkit/drs/model/AccessMethod.java
deleted file mode 100644
index 9a1a49d3..00000000
--- a/deprecated/starterkit/drs/model/AccessMethod.java
+++ /dev/null
@@ -1,144 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.springframework.lang.NonNull;
-
-/**
- * Directly from DRS specification, indicates how to obtain file bytes for a 
- * DRSObject
- */
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class AccessMethod {
-    /**
-     * At least one of accessId or accessUrl is required
-     */
-    private String accessId;
-
-    private AccessURL accessUrl;
-
-    // Required
-    @NonNull
-    private AccessType type;
-
-    // Optional
-    private String region;
-
-    /**
-     * Instantiates a new AccessMethod with empty properties
-     */
-    public AccessMethod() {
-        
-    }
-
-    /**
-     * Instantiates a new AccessMethod with preconfigured accessID and access type
-     * @param accessID access ID
-     * @param type access type
-     */
-    public AccessMethod(String accessID, AccessType type) {
-        this.accessId = accessID;
-        this.type = type;
-    }
-
-    /**
-     * Instantiates a new AccessMethod with preconfigured accessURL and access type
-     * @param accessURL access URL
-     * @param type access type
-     */
-    public AccessMethod(AccessURL accessURL, AccessType type) {
-        this.accessUrl = accessURL;
-        this.type = type;
-    }
-
-    /**
-     * Instantiates a new AccessMethod with preconfigured accessID, access type, and region
-     * @param accessID access ID
-     * @param type access type
-     * @param region region
-     */
-    public AccessMethod(String accessID, AccessType type, String region) {
-        this(accessID, type);
-        this.region = region;
-    }
-
-    /**
-     * Instantiates a new AccessMethod with preconfigured access URL, access type, and region
-     * @param accessURL access URL
-     * @param type access type
-     * @param region region
-     */
-    public AccessMethod(AccessURL accessURL, AccessType type, String region) {
-        this(accessURL, type);
-        this.region = region;
-    }
-
-    /**
-     * Retrieve accessID
-     * @return accessID
-     */
-    public String getAccessId() {
-        return accessId;
-    }
-
-    /**
-     * Assign accessID
-     * @param accessId accessID
-     */
-    public void setAccessId(String accessId) {
-        this.accessId = accessId;
-    }
-
-    /**
-     * Retrieve access URL
-     * @return access URL
-     */
-    public AccessURL getAccessUrl() {
-        return accessUrl;
-    }
-
-    /**
-     * Assign access URL
-     * @param accessUrl access URL
-     */
-    public void setAccessUrl(AccessURL accessUrl) {
-        this.accessUrl = accessUrl;
-    }
-
-    /**
-     * Retrieve access type
-     * @return access type
-     */
-    public AccessType getType() {
-        return type;
-    }
-
-    /**
-     * Assign access type
-     * @param type access type
-     */
-    public void setType(AccessType type) {
-        this.type = type;
-    }
-
-    /**
-     * Retrieve region
-     * @return region
-     */
-    public String getRegion() {
-        return region;
-    }
-
-    /**
-     * Assign region
-     * @param region region
-     */
-    public void setRegion(String region) {
-        this.region = region;
-    }
-}
diff --git a/deprecated/starterkit/drs/model/AccessType.java b/deprecated/starterkit/drs/model/AccessType.java
deleted file mode 100644
index 90af0e3f..00000000
--- a/deprecated/starterkit/drs/model/AccessType.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-
-/**
- * Directly from DRS specification, enumeration of different Access Types for
- * AccessMethods under a DRSObject. Access Types correspond closely with URL
- * schemes for fetching file bytes (e.g. file://, https://, s3://, etc.)
- */
-@JsonNaming(PropertyNamingStrategies.LowerCaseStrategy.class)
-public enum AccessType {
-    // TODO: incorporate other data source schemes, for now only file, s3, https
-    s3,
-    // GS,
-    // FTP,
-    // GSIFTP,
-    // GLOBUS,
-    // HTSGET,
-    https,
-    file,
-}
diff --git a/deprecated/starterkit/drs/model/AccessURL.java b/deprecated/starterkit/drs/model/AccessURL.java
deleted file mode 100644
index 6e66ec68..00000000
--- a/deprecated/starterkit/drs/model/AccessURL.java
+++ /dev/null
@@ -1,79 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.springframework.lang.NonNull;
-import java.net.URI;
-import java.util.Map;
-
-/**
- * Directly from DRS specification, contains URL and headers necessary for 
- * fetching file bytes of a requested DRSObject
- */
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonView(SerializeView.Public.class)
-public class AccessURL {
-
-    @NonNull
-    private URI url;
-
-    private Map<String, String> headers;
-
-    /**
-     * Instantiates a new AccessURL object with default properties
-     */
-    public AccessURL() {
-        
-    }
-
-    /**
-     * Instantiates a new AccessURL object with preconfigured URL
-     * @param url URL to file bytes
-     */
-    public AccessURL(URI url) {
-        this.url = url;
-    }
-
-    /**
-     * Instantiates a new AccessURL object with preconfigured URL and headers
-     * @param url URL to file bytes
-     * @param headers headers to be provided in request to facilitate access to data (eg Auth)
-     */
-    public AccessURL(URI url, Map<String, String> headers) {
-        this.url = url;
-        this.headers = headers;
-    }
-
-    /**
-     * Retrieve URL
-     * @return URL
-     */
-    public URI getUrl() {
-        return url;
-    }
-
-    /**
-     * Assign URL
-     * @param url URL
-     */
-    public void setUrl(URI url) {
-        this.url = url;
-    }
-
-    /**
-     * Retrieve headers
-     * @return headers
-     */
-    public Map<String, String> getHeaders() {
-        return headers;
-    }
-
-    /**
-     * Assign headers
-     * @param headers headers
-     */
-    public void setHeaders(Map<String, String> headers) {
-        this.headers = headers;
-    }
-}
diff --git a/deprecated/starterkit/drs/model/AuthInfo.java b/deprecated/starterkit/drs/model/AuthInfo.java
deleted file mode 100644
index 920bbe28..00000000
--- a/deprecated/starterkit/drs/model/AuthInfo.java
+++ /dev/null
@@ -1,33 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-
-import lombok.Getter;
-import lombok.Setter;
-
-// Authorization information for a single DRS object
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-public class AuthInfo {
-
-    @JsonView(SerializeView.Always.class)
-    private List<AuthType> supportedTypes;
-
-    @JsonView(SerializeView.Always.class)
-    private List<AuthIssuer> passportAuthIssuers;
-
-    public AuthInfo() {
-        supportedTypes = new ArrayList<>();
-        passportAuthIssuers = new ArrayList<>();
-    }
-}
diff --git a/deprecated/starterkit/drs/model/AuthIssuer.java b/deprecated/starterkit/drs/model/AuthIssuer.java
deleted file mode 100644
index 139d452d..00000000
--- a/deprecated/starterkit/drs/model/AuthIssuer.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-public class AuthIssuer {
-
-    @JsonView(SerializeView.Always.class)
-    private String brokerUrl;
-
-    @JsonView(SerializeView.Always.class)
-    private String visaName;
-    
-    @JsonView(SerializeView.Always.class)
-    private String visaIssuer;
-}
diff --git a/deprecated/starterkit/drs/model/AuthType.java b/deprecated/starterkit/drs/model/AuthType.java
deleted file mode 100644
index e8dcdaed..00000000
--- a/deprecated/starterkit/drs/model/AuthType.java
+++ /dev/null
@@ -1,8 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-public enum AuthType {
-    None,
-    BasicAuth,
-    BearerAuth,
-    PassportAuth
-}
diff --git a/deprecated/starterkit/drs/model/AwsS3AccessObject.java b/deprecated/starterkit/drs/model/AwsS3AccessObject.java
deleted file mode 100644
index 3699b312..00000000
--- a/deprecated/starterkit/drs/model/AwsS3AccessObject.java
+++ /dev/null
@@ -1,171 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.io.Serializable;
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.GeneratedValue;
-import javax.persistence.GenerationType;
-import javax.persistence.Id;
-import javax.persistence.JoinColumn;
-import javax.persistence.ManyToOne;
-import javax.persistence.Table;
-import com.fasterxml.jackson.annotation.JsonBackReference;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-
-/**
- * Inferred from DRS specification, indicates byte source for a DRSObject with
- * an 's3' access type. References a file stored on AWS S3. Contains required
- * info to facilitate access to an s3 file/object.
- */
-@Entity
-@Table(name = "aws_s3_access_object")
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Admin.class)
-public class AwsS3AccessObject implements Serializable, HibernateEntity<Long> {
-
-    public static final long serialVersionUID = 1L;
-
-    /**
-     * unique identifier
-     */
-    @Id
-    @Column(name = "id")
-    @GeneratedValue(strategy = GenerationType.IDENTITY)
-    @JsonIgnore
-    private Long id;
-
-    /**
-     * AWS region where bucket is hosted 
-     */
-    @Column(name = "region")
-    private String region;
-
-    /**
-     * AWS S3 bucket name hosting the object
-     */
-    @Column(name = "bucket")
-    private String bucket;
-
-    /**
-     * The key/file path to the object bytes
-     */
-    @Column(name = "key")
-    private String key;
-
-    /**
-     * The DRSObject associated with this access object
-     */
-    @ManyToOne(fetch = FetchType.EAGER,
-               cascade = {CascadeType.PERSIST, CascadeType.MERGE,
-                          CascadeType.DETACH, CascadeType.REFRESH})
-    @JoinColumn(name = "drs_object_id")
-    @JsonBackReference
-    private DrsObject drsObject;
-
-    /* Constructors */
-
-    /**
-     * Instantiates a new AwsS3AccessObject
-     */
-    public AwsS3AccessObject() {
-
-    }
-
-    /**
-     * Fetch relational data that is not loaded automatically (lazy load)
-     */
-    public void loadRelations() {
-
-    }
-
-    /* Setters and Getters */
-
-    /**
-     * Assign id
-     * @param id identifier
-     */
-    public void setId(Long id) {
-        this.id = id;
-    }
-
-    /**
-     * Retrieve id
-     * @return identifier
-     */
-    public Long getId() {
-        return id;
-    }
-
-    /**
-     * Assign region
-     * @param region AWS region
-     */
-    public void setRegion(String region) {
-        this.region = region;
-    }
-
-    /**
-     * Retrieve region
-     * @return AWS region
-     */
-    public String getRegion() {
-        return region;
-    }
-
-    /**
-     * Assign bucket
-     * @param bucket AWS bucket
-     */
-    public void setBucket(String bucket) {
-        this.bucket = bucket;
-    }
-
-    /**
-     * Retrieve bucket
-     * @return AWS bucket
-     */
-    public String getBucket() {
-        return bucket;
-    }
-
-    /**
-     * Assign key
-     * @param key key/file path to object bytes
-     */
-    public void setKey(String key) {
-        this.key = key;
-    }
-
-    /**
-     * Retrieve key
-     * @return key/file path to object bytes
-     */
-    public String getKey() {
-        return key;
-    }
-
-    /**
-     * Assign drsObject
-     * @param drsObject DrsObject associated with this access object
-     */
-    public void setDrsObject(DrsObject drsObject)  {
-        this.drsObject = drsObject;
-    }
-
-    /**
-     * Retrieve drsObject
-     * @return DrsObject associated with this access object
-     */
-    public DrsObject getDrsObject() {
-        return drsObject;
-    }
-}
diff --git a/deprecated/starterkit/drs/model/BulkAccessRequest.java b/deprecated/starterkit/drs/model/BulkAccessRequest.java
deleted file mode 100644
index 84c083d7..00000000
--- a/deprecated/starterkit/drs/model/BulkAccessRequest.java
+++ /dev/null
@@ -1,25 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class BulkAccessRequest {
-    private List<BulkObjectAccessId> selection;
-
-    public BulkAccessRequest() {
-        selection = new ArrayList<>();
-    }
-}
diff --git a/deprecated/starterkit/drs/model/BulkAuthInfoRequest.java b/deprecated/starterkit/drs/model/BulkAuthInfoRequest.java
deleted file mode 100644
index f576ffac..00000000
--- a/deprecated/starterkit/drs/model/BulkAuthInfoRequest.java
+++ /dev/null
@@ -1,24 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.util.ArrayList;
-import java.util.List;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class BulkAuthInfoRequest {
-    private List<String> selection;
-
-    public BulkAuthInfoRequest() {
-        selection = new ArrayList<>();
-    }
-}
diff --git a/deprecated/starterkit/drs/model/BulkAuthInfoResponse.java b/deprecated/starterkit/drs/model/BulkAuthInfoResponse.java
deleted file mode 100644
index fcba244b..00000000
--- a/deprecated/starterkit/drs/model/BulkAuthInfoResponse.java
+++ /dev/null
@@ -1,29 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.util.HashMap;
-import java.util.Map;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class BulkAuthInfoResponse {
-
-    private BulkSummary summary;
-    private Map<String, AuthInfo> resolvedDrsObjectAuthInfo;
-    private Map<String, Integer> unresolvedDrsObjectAuthInfo;
-
-    public BulkAuthInfoResponse() {
-        summary = new BulkSummary();
-        resolvedDrsObjectAuthInfo = new HashMap<>();
-        unresolvedDrsObjectAuthInfo = new HashMap<>();
-    }
-}
diff --git a/deprecated/starterkit/drs/model/BulkObjectAccessId.java b/deprecated/starterkit/drs/model/BulkObjectAccessId.java
deleted file mode 100644
index ffdf077b..00000000
--- a/deprecated/starterkit/drs/model/BulkObjectAccessId.java
+++ /dev/null
@@ -1,21 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import lombok.Getter;
-import lombok.NoArgsConstructor;
-import lombok.Setter;
-
-@Setter
-@Getter
-@NoArgsConstructor
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class BulkObjectAccessId {
-    private String objectId;
-    private String accessId;
-}
diff --git a/deprecated/starterkit/drs/model/BulkRequest.java b/deprecated/starterkit/drs/model/BulkRequest.java
deleted file mode 100644
index 1fadca5b..00000000
--- a/deprecated/starterkit/drs/model/BulkRequest.java
+++ /dev/null
@@ -1,27 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class BulkRequest {
-    private List<String> selection;
-    private List<String> passports;
-
-    public BulkRequest() {
-        selection = new ArrayList<>();
-        passports = new ArrayList<>();
-    }
-}
diff --git a/deprecated/starterkit/drs/model/BulkResponse.java b/deprecated/starterkit/drs/model/BulkResponse.java
deleted file mode 100644
index 35b11a00..00000000
--- a/deprecated/starterkit/drs/model/BulkResponse.java
+++ /dev/null
@@ -1,32 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class BulkResponse {
-
-    private BulkSummary summary;
-    private List<DrsObject> resolvedDrsObject;
-    private Map<String, Integer> unresolvedDrsObject;
-
-    public BulkResponse() {
-        summary = new BulkSummary();
-        resolvedDrsObject = new ArrayList<>();
-        unresolvedDrsObject = new HashMap<>();
-    }
-}
diff --git a/deprecated/starterkit/drs/model/BulkSummary.java b/deprecated/starterkit/drs/model/BulkSummary.java
deleted file mode 100644
index 77066824..00000000
--- a/deprecated/starterkit/drs/model/BulkSummary.java
+++ /dev/null
@@ -1,22 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import lombok.Getter;
-import lombok.NoArgsConstructor;
-import lombok.Setter;
-
-@Setter
-@Getter
-@NoArgsConstructor
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class BulkSummary {
-    private int requested;
-    private int resolved;
-    private int unresolved;
-}
diff --git a/deprecated/starterkit/drs/model/Checksum.java b/deprecated/starterkit/drs/model/Checksum.java
deleted file mode 100644
index 3b84c073..00000000
--- a/deprecated/starterkit/drs/model/Checksum.java
+++ /dev/null
@@ -1,161 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonBackReference;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.springframework.lang.NonNull;
-
-import javax.persistence.*;
-
-/**
- * Directly from DRS specification, indicates a checksum value for a DrsObject's
- * file bytes, as well as the algorithm used.
- */
-@Entity
-@Table(name = "drs_object_checksum")
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Always.class)
-public class Checksum implements HibernateEntity<Long> {
-
-    public static final long serialVersionUID = 1L;
-
-    /**
-     * Unique identifier for checksum in the database
-     */
-    @Id
-    @Column(name = "id")
-    @GeneratedValue(strategy = GenerationType.IDENTITY)
-    @JsonIgnore
-    private Long id;
-
-    /**
-     * Checksum hash value
-     */
-    @Column(name = "checksum")
-    @NonNull
-    private String checksum;
-
-    /**
-     * Hashing algorithm used (eg md5, sha1)
-     */
-    @Column(name = "type")
-    private String type;
-
-    /**
-     * DrsObject that owns this checksum
-     */
-    @ManyToOne(fetch = FetchType.EAGER,
-               cascade = {CascadeType.PERSIST, CascadeType.MERGE,
-                          CascadeType.DETACH, CascadeType.REFRESH})
-    @JoinColumn(name = "drs_object_id", nullable = false, insertable = true, updatable = true)
-    @JsonBackReference
-    private DrsObject drsObject;
-
-    /**
-     * Instantiates a new Checksum
-     */
-    public Checksum() {
-
-    }
-
-    /**
-     * Instantiates a new Checksum with preconfigured id, checksum, and type
-     * @param id unique identifier
-     * @param checksum checksum value
-     * @param type hashing algorithm
-     */
-    public Checksum(Long id, String checksum, String type) {
-        this.id = id;
-        this.checksum = checksum;
-        this.type = type;
-    }
-
-    /**
-     * Instantiates a new Checksum with preconfigured checksum, type, and drsObject
-     * @param checksum checksum value
-     * @param type hashing algorithm
-     * @param drsObject drsObject to which checksum belongs
-     */
-    public Checksum(String checksum, String type, DrsObject drsObject) {
-        this.checksum = checksum;
-        this.type = type;
-        this.drsObject = drsObject;
-    }
-
-    /**
-     * Fetch relational data that is not loaded automatically (lazy load)
-     */
-    public void loadRelations() {
-
-    }
-
-    /**
-     * Assign id
-     * @param id identifier
-     */
-    public void setId(Long id) {
-        this.id = id;
-    }
-
-    /**
-     * Retrieve id
-     * @return identifier
-     */
-    public Long getId() {
-        return id;
-    }
-
-    /**
-     * Assign checksum
-     * @param checksum checksum value
-     */
-    public void setChecksum(String checksum) {
-        this.checksum = checksum;
-    }
-
-    /**
-     * Retrieve checksum
-     * @return checksum value
-     */
-    public String getChecksum() {
-        return checksum;
-    }
-
-    /**
-     * Assign type
-     * @param type hashing algorithm
-     */
-    public void setType(String type) {
-        this.type = type;
-    }
-
-    /**
-     * Retrieve type
-     * @return hashing algorithm
-     */
-    public String getType() {
-        return type;
-    }
-
-    /**
-     * Assign drsObject
-     * @param drsObject DrsObject owning the checksum
-     */
-    public void setDrsObject(DrsObject drsObject) {
-        this.drsObject = drsObject;
-    }
-
-    /**
-     * Retrieve drsObject
-     * @return DrsObject owning the checksum
-     */
-    public DrsObject getDrsObject() {
-        return drsObject;
-    }
-}
diff --git a/deprecated/starterkit/drs/model/ContentsObject.java b/deprecated/starterkit/drs/model/ContentsObject.java
deleted file mode 100644
index b4221e6e..00000000
--- a/deprecated/starterkit/drs/model/ContentsObject.java
+++ /dev/null
@@ -1,122 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.springframework.lang.NonNull;
-import java.net.URI;
-import java.util.List;
-
-/**
- * Directly from DRS specification, references the nested contents of a DRS
- * bundle 
- */
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class ContentsObject {
-
-    /**
-     * Name of ContentsObject
-     */
-    @NonNull
-    private String name;
-
-    /**
-     * Sub-contents of this ContentsObject, indicating that there is further
-     * nesting. The objects within 'contents' may also contain further contents
-     */
-    private List<ContentsObject> contents;
-
-    /**
-     * Full DRS URL/URI that will enable the loading of this ContentsObject as
-     * a full DRSObject
-     */
-    private List<URI> drsUri;
-
-    /**
-     * DRS id
-     */
-    private String id;
-
-    /**
-     * Instantiates a new ContentsObject
-     */
-    public ContentsObject() {
-        
-    }
-
-    /**
-     * Instantiates a new ContentsObject with preset name
-     * @param name name of ContentsObject
-     */
-    public ContentsObject(String name) {
-        this.name = name;
-    }
-
-    /**
-     * Retrieve contents
-     * @return list of nested contents objects
-     */
-    public List<ContentsObject> getContents() {
-        return contents;
-    }
-
-    /**
-     * Assign contents
-     * @param contents list of nested contents objects
-     */
-    public void setContents(List<ContentsObject> contents) {
-        this.contents = contents;
-    }
-
-    /**
-     * Retrieve name
-     * @return name of contents object
-     */
-    public String getName() {
-        return name;
-    }
-
-    /**
-     * Assign name
-     * @param name name of contents object
-     */
-    public void setName(String name) {
-        this.name = name;
-    }
-
-    /**
-     * Retrieve DRS URI
-     * @return DRS URI enabling access to DRSObject outlined by this contents object
-     */
-    public List<URI> getDrsUri() {
-        return drsUri;
-    }
-
-    /**
-     * Assign DRS URI
-     * @param drsUri DRS URI enabling access to DRSObject outlined by this contents object
-     */
-    public void setDrsUri(List<URI> drsUri) {
-        this.drsUri = drsUri;
-    }
-
-    /**
-     * Retrieve id
-     * @return DRS identifier
-     */
-    public String getId() {
-        return id;
-    }
-
-    /**
-     * Assign id
-     * @param id DRS identifier
-     */
-    public void setId(String id) {
-        this.id = id;
-    }
-}
diff --git a/deprecated/starterkit/drs/model/DrsObject.java b/deprecated/starterkit/drs/model/DrsObject.java
deleted file mode 100644
index 55a28571..00000000
--- a/deprecated/starterkit/drs/model/DrsObject.java
+++ /dev/null
@@ -1,259 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonFormat;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonManagedReference;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonDeserialize;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import com.fasterxml.jackson.databind.annotation.JsonSerialize;
-import com.fasterxml.jackson.datatype.jsr310.deser.LocalDateTimeDeserializer;
-import com.fasterxml.jackson.datatype.jsr310.ser.LocalDateTimeSerializer;
-import lombok.Getter;
-import lombok.Setter;
-import org.ga4gh.starterkit.common.constant.DateTimeConstants;
-import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.hibernate.Hibernate;
-import org.hibernate.annotations.Cascade;
-import org.hibernate.annotations.CascadeType;
-import org.springframework.lang.NonNull;
-
-import javax.persistence.*;
-import java.net.URI;
-import java.time.LocalDateTime;
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Directly from DRS specification, with modifications, contains all metadata for
- * a DRSObject as described in the spec. Database (entity) attributes do not 
- * completely align with spec attributes where more relational sophistication
- * is warranted. Entity attributes can be converted to transient attributes that
- * align with and fulfill the DRS spec
- */
-@Entity
-@Table(name = "drs_object")
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-public class DrsObject implements HibernateEntity<String> {
-    
-    /*
-        Simple attributes lifted directly from the DRS spec: id, description,
-        createdTime, mimeType, name, size, updatedTime, version, aliases,
-        checksums
-    */
-
-    @Id
-    @Column(name = "id", updatable = false, nullable = false)
-    @NonNull
-    @JsonView(SerializeView.Always.class)
-    private String id;
-
-    @Column(name = "description")
-    @JsonView(SerializeView.Always.class)
-    private String description;
-
-    @Column(name = "created_time")
-    @JsonDeserialize(using = LocalDateTimeDeserializer.class)
-    @JsonSerialize(using = LocalDateTimeSerializer.class)
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = DateTimeConstants.DATE_FORMAT)
-    @NonNull
-    @JsonView(SerializeView.Always.class)
-    private LocalDateTime createdTime;
-
-    @Column(name = "mime_type")
-    @JsonView(SerializeView.Always.class)
-    private String mimeType;
-
-    @Column(name = "name")
-    @JsonView(SerializeView.Always.class)
-    private String name;
-
-    @Column(name = "size")
-    @JsonView(SerializeView.Always.class)
-    private Long size;
-
-    @Column(name = "updated_time")
-    @JsonDeserialize(using = LocalDateTimeDeserializer.class)
-    @JsonSerialize(using = LocalDateTimeSerializer.class)
-    @JsonFormat(shape = JsonFormat.Shape.STRING, pattern = DateTimeConstants.DATE_FORMAT)
-    @JsonView(SerializeView.Always.class)
-    private LocalDateTime updatedTime;
-
-    @Column(name = "version")
-    @JsonView(SerializeView.Always.class)
-    private String version;
-
-    @ElementCollection(fetch = FetchType.LAZY)
-    @CollectionTable(name = "drs_object_alias", joinColumns = @JoinColumn(name = "drs_object_id"))
-    @Column(name = "alias")
-    @Cascade(value = {CascadeType.ALL})
-    @JsonView({
-        SerializeView.Public.class,
-        SerializeView.Admin.class
-    })
-    private List<String> aliases;
-
-    @OneToMany(mappedBy = "drsObject",
-               fetch = FetchType.LAZY,
-               cascade = {javax.persistence.CascadeType.ALL},
-               orphanRemoval = true)
-    @JsonView({
-        SerializeView.Public.class,
-        SerializeView.Admin.class
-    })
-    @JsonManagedReference
-    private List<Checksum> checksums;
-
-    /* 
-        Attributes capturing the parent-child relationship of DRS bundles to
-        nested/sub bundles, to single blob DRS Objects
-    */
-
-    @Column(name = "is_bundle")
-    @NonNull
-    @JsonView(SerializeView.Admin.class)
-    private Boolean isBundle;
-
-    /**
-     * List of bundles to which this DRSObject belongs, ie its 'parents'
-     */
-    @ManyToMany
-    @JoinTable(
-        name = "drs_object_bundle",
-        joinColumns = {@JoinColumn(name = "parent_id")},
-        inverseJoinColumns = {@JoinColumn(name = "child_id")}
-    )
-    @JsonView(SerializeView.Admin.class)
-    private List<DrsObject> drsObjectChildren;
-
-    /**
-     * List of sub-bundles and/or objects that this bundle has, ie its 'children'
-     */
-    @ManyToMany
-    @JoinTable(
-        name = "drs_object_bundle",
-        joinColumns = {@JoinColumn(name = "child_id")},
-        inverseJoinColumns = {@JoinColumn(name = "parent_id")}
-    )
-    @JsonView(SerializeView.Admin.class)
-    private List<DrsObject> drsObjectParents;
-
-    /*
-        Attributes capturing multiple byte storage/access locations associated
-        with a single DRSObject
-    */
-
-    /**
-     * List of file-based byte sources, ie files local to server
-     */
-    @OneToMany(mappedBy = "drsObject",
-               fetch = FetchType.LAZY,
-               cascade = javax.persistence.CascadeType.ALL,
-               orphanRemoval = true)
-    @JsonView(SerializeView.Admin.class)
-    @JsonManagedReference
-    private List<FileAccessObject> fileAccessObjects;
-
-    /**
-     * List of s3-based byte sources, ie objects on an AWS S3 bucket
-     */
-    @OneToMany(mappedBy = "drsObject",
-               fetch = FetchType.LAZY,
-               cascade = javax.persistence.CascadeType.ALL,
-               orphanRemoval = true)
-    @JsonView(SerializeView.Admin.class)
-    @JsonManagedReference
-    private List<AwsS3AccessObject> awsS3AccessObjects;
-
-    @ManyToMany
-    @JoinTable(
-        name = "drs_object_visa",
-        joinColumns = {@JoinColumn(name = "drs_object_id")},
-        inverseJoinColumns = {@JoinColumn(name = "visa_id")}
-    )
-    @JsonView(SerializeView.Admin.class)
-    private List<PassportVisa> passportVisas;
-
-    /*
-        Transient attributes produced from transforming database records. They
-        are needed to conform to the DRS spec: selfURI, accessMethods, contents
-    */
-
-    /**
-     * self DRS URI derived from service hostname and DRS object id
-     */
-    @Transient
-    @NonNull
-    @JsonView(SerializeView.Public.class)
-    private URI selfURI;
-
-    /**
-     * access methods derived from all 'AccessObject' subtypes (e.g. FileAccessObjects,
-     * AwsS3AccessObjects)
-     */
-    @Transient
-    @JsonView(SerializeView.Public.class)
-    private List<AccessMethod> accessMethods;
-
-    /**
-     * contents objects derived from 'children' DrsObjects
-     */
-    @Transient
-    @JsonView(SerializeView.Public.class)
-    private List<ContentsObject> contents;
-
-    /**
-     * Instantiates a new DrsObject
-     */
-    public DrsObject() {
-        checksums = new ArrayList<>();
-        fileAccessObjects = new ArrayList<>();
-        awsS3AccessObjects = new ArrayList<>();
-        passportVisas = new ArrayList<>();
-    }
-
-    /* Custom API methods */
-
-    /**
-     * Fetch relational data that is not loaded automatically (lazy load)
-     */
-    public void loadRelations() {
-        Hibernate.initialize(getAliases());
-        Hibernate.initialize(getChecksums());
-        Hibernate.initialize(getDrsObjectChildren());
-        Hibernate.initialize(getDrsObjectParents());
-        Hibernate.initialize(getFileAccessObjects());
-        Hibernate.initialize(getAwsS3AccessObjects());
-        Hibernate.initialize(getPassportVisas());
-    }
-
-    @Override
-    public String toString() {
-        return "DrsObject{" +
-                "id='" + id + '\'' +
-                ", description='" + description + '\'' +
-                ", createdTime=" + createdTime +
-                ", mimeType='" + mimeType + '\'' +
-                ", name='" + name + '\'' +
-                ", size=" + size +
-                ", updatedTime=" + updatedTime +
-                ", version='" + version + '\'' +
-                ", aliases=" + aliases +
-                ", checksums=" + checksums +
-                ", isBundle=" + isBundle +
-                ", drsObjectChildren=" + drsObjectChildren +
-                ", drsObjectParents=" + drsObjectParents +
-                ", fileAccessObjects=" + fileAccessObjects +
-                ", awsS3AccessObjects=" + awsS3AccessObjects +
-                ", passportVisas=" + passportVisas +
-                ", selfURI=" + selfURI +
-                ", accessMethods=" + accessMethods +
-                ", contents=" + contents +
-                '}';
-    }
-}
diff --git a/deprecated/starterkit/drs/model/DrsServiceInfo.java b/deprecated/starterkit/drs/model/DrsServiceInfo.java
deleted file mode 100644
index 240fee06..00000000
--- a/deprecated/starterkit/drs/model/DrsServiceInfo.java
+++ /dev/null
@@ -1,57 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import org.ga4gh.starterkit.common.model.ServiceInfo;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ID;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.NAME;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.DESCRIPTION;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.CONTACT_URL;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.DOCUMENTATION_URL;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.CREATED_AT;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.UPDATED_AT;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ENVIRONMENT;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.VERSION;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ORGANIZATION_NAME;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.ORGANIZATION_URL;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_GROUP;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_ARTIFACT;
-import static org.ga4gh.starterkit.drs.constant.DrsServiceInfoDefaults.SERVICE_TYPE_VERSION;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-
-/**
- * Extension of the GA4GH base service info specification to include DRS-specific
- * properties
- */
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.LowerCamelCaseStrategy.class)
-public class DrsServiceInfo extends ServiceInfo {
-
-    /**
-     * Instantiates a new DrsServiceInfo object
-     */
-    public DrsServiceInfo() {
-        super();
-        setAllDefaults();
-    }
-
-    /**
-     * Sets all default properties
-     */
-    private void setAllDefaults() {
-        setId(ID);
-        setName(NAME);
-        setDescription(DESCRIPTION);
-        setContactUrl(CONTACT_URL);
-        setDocumentationUrl(DOCUMENTATION_URL);
-        setCreatedAt(CREATED_AT);
-        setUpdatedAt(UPDATED_AT);
-        setEnvironment(ENVIRONMENT);
-        setVersion(VERSION);
-        getOrganization().setName(ORGANIZATION_NAME);
-        getOrganization().setUrl(ORGANIZATION_URL);
-        getType().setGroup(SERVICE_TYPE_GROUP);
-        getType().setArtifact(SERVICE_TYPE_ARTIFACT);
-        getType().setVersion(SERVICE_TYPE_VERSION);
-    }
-}
diff --git a/deprecated/starterkit/drs/model/Error.java b/deprecated/starterkit/drs/model/Error.java
deleted file mode 100644
index d365993c..00000000
--- a/deprecated/starterkit/drs/model/Error.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-
-/**
- * Directly from DRS specification, error object returned to client whenever a
- * server or client-side error is encountered during a DRS controller function
- */
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-public class Error extends Exception {
-
-    public static final long serialVersionUID = 1L;
-
-    private String msg;
-
-    private int statusCode;
-
-    /**
-     * Instantiates a new Error
-     * @param message helpful error message
-     * @param statusCode HTTP status code
-     */
-    public Error(String message, int statusCode) {
-        this.msg = message;
-        this.statusCode = statusCode;
-    }
-
-    /**
-     * Retrieve msg
-     * @return error message
-     */
-    public String getMsg() {
-        return msg;
-    }
-
-    /**
-     * Retrieve full message for logging purposes
-     * @return message indicating error code and msg
-     */
-    public String getMessage() {
-        return "status_code: " + statusCode + " message: " + msg;
-    }
-
-    /**
-     * Assign msg
-     * @param msg error message
-     */
-    public void setMsg(String msg) {
-        this.msg = msg;
-    }
-
-    /**
-     * Retrieve status code
-     * @return HTTP status code
-     */
-    public int getStatusCode() {
-        return statusCode;
-    }
-
-    /**
-     * Assign statusCode
-     * @param statusCode HTTP status code
-     */
-    public void setStatusCode(int statusCode) {
-        this.statusCode = statusCode;
-    }
-}
diff --git a/deprecated/starterkit/drs/model/FileAccessObject.java b/deprecated/starterkit/drs/model/FileAccessObject.java
deleted file mode 100644
index 36276301..00000000
--- a/deprecated/starterkit/drs/model/FileAccessObject.java
+++ /dev/null
@@ -1,122 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonBackReference;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-
-import javax.persistence.*;
-import java.io.Serializable;
-
-/**
- * Inferred from DRS specification, indicates a byte source for a DRSObject with
- * a 'file' access type. References a file that is locally available wherever 
- * the server is deployed. Contains required info to facilitate access to a
- * local file (generally just file path)
- */
-@Entity
-@Table(name = "file_access_object")
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Admin.class)
-public class FileAccessObject implements Serializable, HibernateEntity<Long> {
-
-    public static final long serialVersionUID = 1L;
-
-    @Id
-    @Column(name = "id")
-    @GeneratedValue(strategy = GenerationType.IDENTITY)
-    @JsonIgnore
-    private Long id;
-
-    /**
-     * Local file path
-     */
-    @Column(name = "path")
-    private String path;
-
-    @ManyToOne(fetch = FetchType.EAGER,
-               cascade = {CascadeType.PERSIST, CascadeType.MERGE,
-                          CascadeType.DETACH, CascadeType.REFRESH})
-    @JoinColumn(name = "drs_object_id")
-    @JsonBackReference
-    private DrsObject drsObject;
-
-    /* Constructors */
-
-    /**
-     * Instantiates a new FileAccessObject
-     */
-    public FileAccessObject() {
-
-    }
-
-    /**
-     * Instantiates a new FileAccessObject with parameters
-     */
-    public FileAccessObject(DrsObject drsObject, String filePath) {
-        this.drsObject = drsObject;
-        this.path = filePath;
-    }
-
-    /**
-     * Fetch relational data that is not loaded automatically (lazy load)
-     */
-    public void loadRelations() {
-        
-    }
-
-    /* Setters and Getters */
-
-    /**
-     * Assign id
-     * @param id identifier
-     */
-    public void setId(Long id) {
-        this.id = id;
-    }
-
-    /**
-     * Retrieve id
-     * @return identifier
-     */
-    public Long getId() {
-        return id;
-    }
-
-    /**
-     * Assign path
-     * @param path local file path
-     */
-    public void setPath(String path) {
-        this.path = path;
-    }
-
-    /**
-     * Retrive path
-     * @return local file path
-     */
-    public String getPath() {
-        return path;
-    }
-
-    /**
-     * Assign drsObject
-     * @param drsObject DrsObject owning this access object
-     */
-    public void setDrsObject(DrsObject drsObject) {
-        this.drsObject = drsObject;
-    }
-
-    /**
-     * Retrieve drsObject
-     * @return DrsObject owning this access object
-     */
-    public DrsObject getDrsObject() {
-        return drsObject;
-    }
-}
diff --git a/deprecated/starterkit/drs/model/PassportBroker.java b/deprecated/starterkit/drs/model/PassportBroker.java
deleted file mode 100644
index 0bba67fe..00000000
--- a/deprecated/starterkit/drs/model/PassportBroker.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.persistence.CascadeType;
-import javax.persistence.Column;
-import javax.persistence.Entity;
-import javax.persistence.FetchType;
-import javax.persistence.Id;
-import javax.persistence.OneToMany;
-import javax.persistence.Table;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-
-import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.hibernate.Hibernate;
-import org.springframework.lang.NonNull;
-import lombok.Getter;
-import lombok.Setter;
-
-@Entity
-@Table(name = "passport_broker")
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-public class PassportBroker implements HibernateEntity<String> {
-
-    @Id
-    @Column(name = "url", updatable = false, nullable = false)
-    @NonNull
-    @JsonView(SerializeView.Admin.class)
-    private String url;
-
-    @Column(name = "secret")
-    @JsonView(SerializeView.Admin.class)
-    private String secret;
-
-    @OneToMany(
-        mappedBy = "passportBroker",
-        fetch = FetchType.LAZY,
-        cascade = {CascadeType.ALL},
-        orphanRemoval = true
-    )
-    @JsonView(SerializeView.Never.class)
-    private List<PassportVisa> passportVisas;
-
-    public PassportBroker() {
-        passportVisas = new ArrayList<>();
-    }
-
-    public void setId(String url) {
-        this.url = url;
-    }
-
-    public String getId() {
-        return url;
-    }
-
-    public void loadRelations() {
-        Hibernate.initialize(getPassportVisas());
-    }
-}
diff --git a/deprecated/starterkit/drs/model/PassportVisa.java b/deprecated/starterkit/drs/model/PassportVisa.java
deleted file mode 100644
index 6e0e0798..00000000
--- a/deprecated/starterkit/drs/model/PassportVisa.java
+++ /dev/null
@@ -1,69 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import lombok.Getter;
-import lombok.NonNull;
-import lombok.Setter;
-import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import org.hibernate.Hibernate;
-
-import javax.persistence.*;
-import java.util.ArrayList;
-import java.util.List;
-
-@Entity
-@Table(name = "passport_visa")
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_EMPTY)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-public class PassportVisa implements HibernateEntity<String> {
-
-    @Id
-    @Column(name = "id", updatable = false, nullable = false)
-    @NonNull
-    @JsonView(SerializeView.Admin.class)
-    private String id;
-
-    @Column(name = "name")
-    @JsonView(SerializeView.Admin.class)
-    private String name;
-
-    @Column(name = "issuer")
-    @JsonView(SerializeView.Admin.class)
-    private String issuer;
-
-    @Column(name = "secret")
-    @JsonView(SerializeView.Admin.class)
-    private String secret;
-
-    @ManyToOne(
-        fetch = FetchType.EAGER,
-        cascade = {CascadeType.PERSIST, CascadeType.MERGE,
-                   CascadeType.DETACH, CascadeType.REFRESH}
-    )
-    @JoinColumn(name = "passport_broker_url")
-    @JsonView(SerializeView.Admin.class)
-    private PassportBroker passportBroker;
-
-    @ManyToMany
-    @JoinTable(
-        name = "drs_object_visa",
-        joinColumns = {@JoinColumn(name = "visa_id")},
-        inverseJoinColumns = {@JoinColumn(name = "drs_object_id")}
-    )
-    @JsonView(SerializeView.Never.class)
-    private List<DrsObject> drsObjects;
-
-    public PassportVisa() {
-        drsObjects = new ArrayList<>();
-    }
-
-    public void loadRelations() {
-        Hibernate.initialize(getDrsObjects());
-    }
-}
diff --git a/deprecated/starterkit/drs/model/PostSingleObjectRequestBody.java b/deprecated/starterkit/drs/model/PostSingleObjectRequestBody.java
deleted file mode 100644
index 4e3ce090..00000000
--- a/deprecated/starterkit/drs/model/PostSingleObjectRequestBody.java
+++ /dev/null
@@ -1,26 +0,0 @@
-package org.ga4gh.starterkit.drs.model;
-
-import java.util.ArrayList;
-import java.util.List;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.annotation.JsonView;
-import com.fasterxml.jackson.databind.PropertyNamingStrategies;
-import com.fasterxml.jackson.databind.annotation.JsonNaming;
-import org.ga4gh.starterkit.drs.utils.SerializeView;
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-@JsonInclude(JsonInclude.Include.NON_NULL)
-@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
-@JsonView(SerializeView.Public.class)
-public class PostSingleObjectRequestBody {
-    private boolean expand;
-    private List<String> passports;
-
-    public PostSingleObjectRequestBody() {
-        expand = false;
-        passports = new ArrayList<>();
-    }
-}
diff --git a/deprecated/starterkit/drs/model/package-info.java b/deprecated/starterkit/drs/model/package-info.java
deleted file mode 100644
index b33ec91f..00000000
--- a/deprecated/starterkit/drs/model/package-info.java
+++ /dev/null
@@ -1,10 +0,0 @@
-/**
- * Contains model definitions (under MVC pattern) for DRS-related views and
- * controllers. Contains both database entities and non-entity models. This
- * package attempts to stay closely aligned with model definitions in the DRS
- * spec, but helper classes/entities have been added as needed.
- * 
- * @since 0.1.4
- * @version 0.1.4
- */
-package org.ga4gh.starterkit.drs.model;
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/utils/BundleRecursiveChecksumCalculator.java b/deprecated/starterkit/drs/utils/BundleRecursiveChecksumCalculator.java
deleted file mode 100644
index 052c58a7..00000000
--- a/deprecated/starterkit/drs/utils/BundleRecursiveChecksumCalculator.java
+++ /dev/null
@@ -1,104 +0,0 @@
-package org.ga4gh.starterkit.drs.utils;
-
-import java.util.ArrayList;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import org.ga4gh.starterkit.drs.model.Checksum;
-import org.ga4gh.starterkit.drs.model.DrsObject;
-import org.apache.commons.codec.digest.DigestUtils;
-import org.apache.commons.codec.digest.MessageDigestAlgorithms;
-import org.apache.commons.lang3.StringUtils;
-
-/* Recursively calculates checksum values for bundle-based DrsObjects based on 
- * the checksums of the blob-based DrsObject children it has
- */
-public class BundleRecursiveChecksumCalculator {
-
-    public static List<Checksum> getChecksums(DrsObject drsObject) {
-        return checksumMapToList(recursiveCalculateChecksums(drsObject));
-    }
-
-    public static Map<String, String> recursiveCalculateChecksums(DrsObject parentDrsObject) {
-        Map<String, String> checksumMap = null;
-        List<DrsObject> childrenDrsObjects = parentDrsObject.getDrsObjectChildren();
-
-        if (childrenDrsObjects != null) {
-            if (childrenDrsObjects.size() == 0) {
-                checksumMap = createChecksumMapFromDrsObjectBlob(parentDrsObject);
-            } else {
-                List<Map<String, String>> childChecksumMaps = new ArrayList<>();
-                for (int i = 0; i < childrenDrsObjects.size(); i++) {
-                    childChecksumMaps.add(recursiveCalculateChecksums(childrenDrsObjects.get(i)));
-                }
-                checksumMap = mergeChecksumMaps(childChecksumMaps);
-            }
-        }
-        return checksumMap;
-    }
-
-    private static List<Checksum> checksumMapToList(Map<String, String> checksumMap) {
-        List<Checksum> checksumList = new ArrayList<>();
-        for (String key : checksumMap.keySet()) {
-            Checksum checksum = new Checksum();
-            checksum.setType(key);
-            checksum.setChecksum(checksumMap.get(key));
-            checksumList.add(checksum);
-        }
-        return checksumList;
-    }
-
-    private static Map<String, String> createChecksumMapFromDrsObjectBlob(DrsObject drsObject) {
-        Map<String, String> checksumMap = new HashMap<>();
-        for (Checksum checksum: drsObject.getChecksums()) {
-            checksumMap.put(checksum.getType(), checksum.getChecksum());
-        }
-        return checksumMap;
-    }
-
-    private static Map<String, String> mergeChecksumMaps(List<Map<String, String>> checksumMaps) {
-        // initial setup
-        Map<String, String> mergedChecksumMap = new HashMap<>();
-        Map<String, Integer> checksumTypeCounts = new HashMap<>();
-        int nMaps = checksumMaps.size();
-
-        // first loop, determine the checksum types shared by all children
-        for (Map<String, String> checksumMap : checksumMaps) {
-            for (String key : checksumMap.keySet()) {
-                if (!checksumTypeCounts.containsKey(key)) {
-                    checksumTypeCounts.put(key, 0);
-                }
-                checksumTypeCounts.put(key, checksumTypeCounts.get(key) + 1);
-            }
-        }
-
-        // second loop, for each final checksum type, sort and concatenate values
-        for (String key : checksumTypeCounts.keySet()) {
-            if (checksumTypeCounts.get(key) == nMaps) {
-                List<String> checksumValues = new ArrayList<>();
-                for (Map<String, String> checksumMap : checksumMaps) {
-                    checksumValues.add(checksumMap.get(key));
-                }
-                Collections.sort(checksumValues);
-                String concatenated = StringUtils.join(checksumValues, "");
-
-                String algorithm = null;
-                switch (key) {
-                    case "md5":
-                        algorithm = MessageDigestAlgorithms.MD5;
-                        break;
-                    case "sha1":
-                        algorithm = MessageDigestAlgorithms.SHA_1;
-                        break;
-                    case "sha256":
-                        algorithm = MessageDigestAlgorithms.SHA_256;
-                        break;
-                }
-                String concatDigest = new DigestUtils(algorithm).digestAsHex(concatenated);
-                mergedChecksumMap.put(key, concatDigest);
-            }
-        }
-        return mergedChecksumMap;
-    }
-}
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/utils/SerializeView.java b/deprecated/starterkit/drs/utils/SerializeView.java
deleted file mode 100644
index fac23e81..00000000
--- a/deprecated/starterkit/drs/utils/SerializeView.java
+++ /dev/null
@@ -1,31 +0,0 @@
-package org.ga4gh.starterkit.drs.utils;
-
-/**
- * Enables flexible serialization of different model attributes based on controller
- * function. Used with the @JsonView annotation on controller functions and
- * model properties to align serialized attributes with specific endpoints
- */
-public class SerializeView {
-
-    /**
-     * The attribute will always be serialized
-     */
-    public static class Always {}
-
-    /**
-     * The attribute will only be serialized for controllers marked 'Public',
-     * that is, pertaining to the public (non admin) API
-     */
-    public static class Public extends Always {}
-
-    /**
-     * The attribute will only be serialized for controllers marked 'Admin',
-     * that is, pertaining to private, administrative API routes
-     */
-    public static class Admin extends Always {}
-
-    /**
-     * The attribute will never be serialized
-     */
-    public static class Never {}
-}
diff --git a/deprecated/starterkit/drs/utils/cache/AccessCache.java b/deprecated/starterkit/drs/utils/cache/AccessCache.java
deleted file mode 100644
index 1a9211c0..00000000
--- a/deprecated/starterkit/drs/utils/cache/AccessCache.java
+++ /dev/null
@@ -1,69 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.cache;
-
-import com.google.common.cache.CacheBuilder;
-import com.google.common.cache.CacheLoader;
-import com.google.common.cache.LoadingCache;
-
-/**
- * Cache singleton storing information mapping DRS Object ids and access ids
- * to the byte source for a requested DRSObject
- */
-public class AccessCache {
-
-    /**
-     * a cache mapping DRSObject + access id to richer AccessCacheItem info
-     */
-    private LoadingCache<String, AccessCacheItem> cache;
-
-    /**
-     * Instantiates a new AccessCache
-     */
-    public AccessCache() {
-        buildCache();
-    }
-
-    /**
-     * Builds the cache
-     */
-    private void buildCache() {
-        cache = CacheBuilder.newBuilder()
-            .maximumSize(1000)
-            .build(
-                new CacheLoader<String, AccessCacheItem>(){
-                    public AccessCacheItem load(String key) {
-                        return new AccessCacheItem();
-                    }
-                }
-            );
-    }
-
-    /**
-     * Add a new item to the cache
-     * @param objectId DRS Object id
-     * @param accessId access id
-     * @param value the access cache item providing info on how to access the bytes
-     */
-    public void put(String objectId, String accessId, AccessCacheItem value) {
-        cache.put(getCompositeKey(objectId, accessId), value);
-    }
-
-    /**
-     * Retrieve an item from the cache
-     * @param objectId DRS Object id
-     * @param accessId access id
-     * @return the access cache item for the given ids, provides info on how to access the bytes
-     */
-    public AccessCacheItem get(String objectId, String accessId) {
-        return cache.getIfPresent(getCompositeKey(objectId, accessId));
-    }
-
-    /**
-     * Construct a key for the cache based on DRS Object id and access id
-     * @param objectId DRS Object id
-     * @param accessId access id
-     * @return a composite id constructed from both ids
-     */
-    private String getCompositeKey(String objectId, String accessId) {
-        return objectId.toString() + ":" + accessId;
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/cache/AccessCacheItem.java b/deprecated/starterkit/drs/utils/cache/AccessCacheItem.java
deleted file mode 100644
index fcc5220c..00000000
--- a/deprecated/starterkit/drs/utils/cache/AccessCacheItem.java
+++ /dev/null
@@ -1,103 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.cache;
-
-import org.ga4gh.starterkit.drs.model.AccessType;
-
-/**
- * A single item within the access cache, stores information on how to access
- * the file bytes for a composite DRSObject id + access id
- */
-public class AccessCacheItem {
-
-    private String objectId;
-    private String accessId;
-    private String objectPath;
-    private AccessType accessType;
-    private String mimeType;
-
-    /**
-     * Instantiates a new AccessCacheItem
-     */
-    public AccessCacheItem() {
-
-    }
-
-    /**
-     * Assign objectId
-     * @param objectId DRSObject id
-     */
-    public void setObjectId(String objectId) {
-        this.objectId = objectId;
-    }
-
-    /**
-     * Retrieve objectId
-     * @return DRSObject id
-     */
-    public String getObjectId() {
-        return objectId;
-    }
-
-    /**
-     * Assign accessId
-     * @param accessId access id
-     */
-    public void setAccessId(String accessId) {
-        this.accessId = accessId;
-    }
-
-    /**
-     * Retrieve accessId
-     * @return access id
-     */
-    public String getAccessId() {
-        return accessId;
-    }
-
-    /**
-     * Assign objectPath
-     * @param objectPath path to the file bytes
-     */
-    public void setObjectPath(String objectPath) {
-        this.objectPath = objectPath;
-    }
-
-    /**
-     * Retrieve objectPath
-     * @return path to the file bytes
-     */
-    public String getObjectPath() {
-        return objectPath;
-    }
-
-    /**
-     * Assign accessType
-     * @param accessType access type for file byte source (ie URL scheme)
-     */
-    public void setAccessType(AccessType accessType) {
-        this.accessType = accessType;
-    }
-
-    /**
-     * Retrieve accessType
-     * @return access type for file byte source (ie URL scheme)
-     */
-    public AccessType getAccessType() {
-        return accessType;
-    }
-
-    /**
-     * Assign mimeType
-     * @param mimeType valid media type
-     */
-    public void setMimeType(String mimeType) {
-        this.mimeType = mimeType;
-    }
-
-    /**
-     * Retrieve mimeType
-     * @return valid media type
-     */
-    public String getMimeType() {
-        return mimeType;
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/cache/package-info.java b/deprecated/starterkit/drs/utils/cache/package-info.java
deleted file mode 100644
index 0d06893c..00000000
--- a/deprecated/starterkit/drs/utils/cache/package-info.java
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * Contains the access cache and related classes, which facilitates access to
- * access URLs via a constructed access ID according to the DRS spec.
- */
-package org.ga4gh.starterkit.drs.utils.cache;
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/utils/hibernate/DrsHibernateUtil.java b/deprecated/starterkit/drs/utils/hibernate/DrsHibernateUtil.java
deleted file mode 100644
index 0665b1f2..00000000
--- a/deprecated/starterkit/drs/utils/hibernate/DrsHibernateUtil.java
+++ /dev/null
@@ -1,330 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.hibernate;
-
-import org.ga4gh.starterkit.common.hibernate.HibernateEntity;
-import org.ga4gh.starterkit.common.hibernate.HibernateUtil;
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
-import org.ga4gh.starterkit.drs.model.Checksum;
-import org.ga4gh.starterkit.drs.model.DrsObject;
-import org.ga4gh.starterkit.drs.model.FileAccessObject;
-import org.ga4gh.starterkit.drs.model.PassportVisa;
-import org.ga4gh.starterkit.drs.utils.BundleRecursiveChecksumCalculator;
-import org.hibernate.HibernateException;
-import org.hibernate.Session;
-import org.hibernate.SessionFactory;
-import org.hibernate.Transaction;
-import org.hibernate.query.Query;
-import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.web.multipart.MultipartFile;
-
-import javax.persistence.PersistenceException;
-import javax.persistence.criteria.CriteriaBuilder;
-import javax.persistence.criteria.CriteriaQuery;
-import javax.persistence.criteria.Predicate;
-import javax.persistence.criteria.Root;
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.Serializable;
-import java.lang.reflect.Method;
-import java.time.LocalDateTime;
-import java.time.format.DateTimeFormatter;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.concurrent.*;
-import java.util.stream.Collectors;
-import java.util.stream.Stream;
-
-/**
- * Provides access to DRS entities/tables in the database, enabling access, creation,
- * updating, and deleting of DRSObjects and associated entities
- */
-public class DrsHibernateUtil extends HibernateUtil {
-
-    /**
-     * Fully loads a DRS Object, performing recursive inspection/loading of child
-     * objects (in the case of bundles)
-     *
-     * @param id DRSObject identifier
-     * @param recursiveChildLoad if true, recursively load the children of each child until termini DRSObjects have been reached
-     * @return DRSObject with all necessary attributes loaded
-     * @throws HibernateException if problem encountered while interacting with db
-     */
-
-    @Autowired
-    private LoggingUtil loggingUtil;
-
-    @Autowired
-    private HibernateUtil hibernateUtil;
-
-    private SessionFactory sessionFactory;
-
-    public DrsObject loadDrsObject(String id, boolean recursiveChildLoad) throws HibernateException {
-        Session session = newTransaction();
-        DrsObject drsObject = null;
-        try {
-            drsObject = session.get(DrsObject.class, id);
-            if (drsObject != null) {
-                drsObject.loadRelations();
-
-                // detach entity so computed fields (size, checksum)
-                // aren't saved to db
-                session.evict(drsObject);
-                if (recursiveChildLoad) {
-                    recursiveDrsObjectChildLoad(drsObject);
-                    drsObject.setSize(recursiveSize(drsObject));
-                    drsObject.setChecksums(BundleRecursiveChecksumCalculator.getChecksums(drsObject));
-                }
-            }
-        } catch (PersistenceException e) {
-            loggingUtil.error("Exception occurred: persistence exception" + e.getMessage());
-            throw new HibernateException(e.getMessage());
-        } catch (Exception e) {
-            loggingUtil.error("Exception occurred: persistence exception" + e.getMessage());
-            throw new HibernateException(e.getMessage());
-        } finally {
-            endTransaction(session);
-        }
-        return drsObject;
-    }
-
-    /**
-     * Recursive function that loads all the children associated to a parent DrsObject.
-     * Recursively calls this function again if a child object has children itself.
-     *
-     * @param parentDrsObject root DRSObject to load all children for
-     * @return byte size sum of all recursive objects under the DrsObject node
-     */
-    private void recursiveDrsObjectChildLoad(DrsObject parentDrsObject) {
-        List<DrsObject> childrenDrsObjects = parentDrsObject.getDrsObjectChildren();
-
-        if (childrenDrsObjects != null) {
-            if (childrenDrsObjects.size() != 0) {
-                for (int i = 0; i < childrenDrsObjects.size(); i++) {
-                    childrenDrsObjects.get(i).loadRelations();
-                    recursiveDrsObjectChildLoad(childrenDrsObjects.get(i));
-                }
-            }
-        }
-    }
-
-    private Long recursiveSize(DrsObject parentDrsObject) {
-        Long sizeSum = 0L;
-        List<DrsObject> childrenDrsObjects = parentDrsObject.getDrsObjectChildren();
-
-        if (childrenDrsObjects != null) {
-            if (childrenDrsObjects.size() == 0) {
-                sizeSum = parentDrsObject.getSize();
-                sizeSum = sizeSum == null ? 0L : sizeSum;
-            } else {
-                for (int i = 0; i < childrenDrsObjects.size(); i++) {
-                    sizeSum += recursiveSize(childrenDrsObjects.get(i));
-                }
-            }
-        }
-        return sizeSum;
-    }
-
-    /**
-     * Retrieve a list of objects from the database
-     *
-     * @param <T>         The entity class to be retrieved
-     * @param entityClass The entity class to be retrieved
-     * @return List of entity objects
-     */
-    public <T extends HibernateEntity<? extends Serializable>> List<T> getEntityList(Class<T> entityClass) {
-        Session session = newTransaction();
-        List<T> entities = null;
-        try {
-            CriteriaBuilder builder = session.getCriteriaBuilder();
-            CriteriaQuery<T> criteria = builder.createQuery(entityClass);
-            criteria.from(entityClass);
-            entities = session.createQuery(criteria).getResultList();
-        } finally {
-            endTransaction(session);
-        }
-        return entities;
-    }
-
-    public PassportVisa findPassportVisa(String visaName, String visaIssuer) {
-        Session session = newTransaction();
-        PassportVisa visa = null;
-        try {
-            CriteriaBuilder cb = session.getCriteriaBuilder();
-            CriteriaQuery<PassportVisa> cq = cb.createQuery(PassportVisa.class);
-            Root<PassportVisa> root = cq.from(PassportVisa.class);
-            Predicate[] predicates = new Predicate[2];
-            predicates[0] = cb.equal(root.get("name"), visaName);
-            predicates[1] = cb.equal(root.get("issuer"), visaIssuer);
-            cq.select(root).where(predicates);
-            Query<PassportVisa> query = session.createQuery(cq);
-            List<PassportVisa> results = query.getResultList();
-            if (results.size() != 1) {
-                String exceptionMessage = "no unique visa found";
-                loggingUtil.error("Exception occurred: " + exceptionMessage);
-                throw new Exception(exceptionMessage);
-            }
-            visa = results.get(0);
-        } catch (Exception ex) {
-            loggingUtil.error("Exception occurred: " + ex.getMessage());
-        } finally {
-            endTransaction(session);
-        }
-        return visa;
-    }
-
-
-    public void insertBulkDrsObjects(MultipartFile file) throws Exception {
-        List<DrsObject> dataToInsert = new ArrayList<DrsObject>();
-        int totalSize = 0;
-        int processedRecords = 0;
-        int successfulRecords = 0;
-        List<DrsObject> failedRecords = new CopyOnWriteArrayList<>();
-
-        try {
-            try (BufferedReader reader = new BufferedReader(new InputStreamReader(file.getInputStream()))) {
-                dataToInsert = prepareDataForInsert(reader);
-                totalSize = dataToInsert.size();
-            } catch (IOException ex) {
-                loggingUtil.error("Exception occurred during read: " + ex);
-            }
-
-            int batchSize = 1000;
-            loggingUtil.info("Starting bulk insert for "+totalSize+" records.");
-            for (int i = 0; i < totalSize; i += batchSize) {
-                int toIndex = Math.min(i + batchSize, totalSize);
-                List<DrsObject> batch = dataToInsert.subList(i, toIndex);
-                failedRecords = performBulkInsertWithExecutor(batch, 8, batchSize, failedRecords);
-
-                int batchFailures = failedRecords.size(); // Capture failed count before next batch
-                successfulRecords += (batch.size() - batchFailures);
-                processedRecords += batch.size();
-                loggingUtil.info("Processed "+processedRecords+" records out of "+totalSize);
-            }
-            loggingUtil.info("Completed bulk insert for "+totalSize+" records.");
-            loggingUtil.info("Inserted: "+ (totalSize - failedRecords.size()));
-            loggingUtil.info("Failed to insert: "+ failedRecords.size());
-        } catch (Exception ex) {
-            loggingUtil.error("Exception during bulk insert: " + ex.getMessage()+ ex);
-            throw ex;
-        }
-    }
-
-    private List<DrsObject> prepareDataForInsert(BufferedReader reader) throws IOException {
-        List<DrsObject> dataToInsert = new ArrayList<>();
-        String row;
-        reader.readLine();
-        DrsObject drsObject = null;
-        while ((row = reader.readLine()) != null) {
-            drsObject = createAndReturnDrsObject(row);
-            dataToInsert.add(drsObject);
-        }
-        return dataToInsert;
-    }
-
-    private DrsObject createAndReturnDrsObject(String line) {
-        String[] fields = line.split(",");
-        String description = Arrays.asList(fields[1].split("/")).get(fields[1].split("/").length-1);
-        DateTimeFormatter formatter = DateTimeFormatter.ofPattern("yyyy-MM-dd'T'HH:mm:ss'Z'");
-
-        DrsObject drsObject = new DrsObject();
-        drsObject.setId(fields[0]);
-        drsObject.setDescription(description);
-        drsObject.setName(description);
-        drsObject.setMimeType(fields[2]);
-        drsObject.setSize(Long.valueOf(fields[3]));
-        drsObject.setUpdatedTime(LocalDateTime.parse(fields[4], formatter));
-        drsObject.setCreatedTime(LocalDateTime.parse(fields[5], formatter));
-        if(fields[1] != null) {
-            List<FileAccessObject> files = createAndReturnFileObjects(drsObject, fields[1]);
-            drsObject.setFileAccessObjects(files);
-        }
-        if(fields[6] != null || fields[7] != null || fields[8] != null) {
-            List<Checksum> checksums = createAndReturnChecksums(drsObject, fields[6], fields[7], fields[8]);
-            drsObject.setChecksums(checksums);
-        }
-
-        return drsObject;
-    }
-
-    private List<Checksum> createAndReturnChecksums(DrsObject drsObject, String cMD5, String cSHA1, String cSHA256) {
-        Checksum md5 = new Checksum(cMD5,"md5", drsObject);
-        Checksum sha1 = new Checksum(cSHA1,"sha1", drsObject);
-        Checksum sha256 = new Checksum(cSHA256,"sha256", drsObject);
-        /*
-        if(drsObject.getId().equals("")) {
-            sha256 = new Checksum(cSHA256,"sha512", drsObject);
-        }
-        */
-
-        return List.of(md5, sha1, sha256);
-    }
-
-    private List<FileAccessObject> createAndReturnFileObjects(DrsObject drsObject, String field) {
-        String[] filePaths = field.split(",");
-        return Stream.of(filePaths)
-                .map(path -> new FileAccessObject(drsObject, path))
-                .collect(Collectors.toList());
-    }
-
-    public <I extends Serializable, T extends HibernateEntity<I>> List<DrsObject> performBulkInsertWithExecutor(
-            List<DrsObject> objectList, int numThreads, int batchSize, List<DrsObject> failedRecords) throws Exception {
-
-        ExecutorService executor = Executors.newFixedThreadPool(numThreads);
-        List<Future<List<DrsObject>>> futures = new ArrayList<>();
-        int totalSize = objectList.size();
-
-        try {
-            for (int i = 0; i < totalSize; i += batchSize) {
-                List<DrsObject> batch = objectList.subList(i, Math.min(i + batchSize, totalSize));
-
-                futures.add(executor.submit(() -> {
-                    List<DrsObject> failedBatch = new ArrayList<>();
-
-                    Session session = null;
-                    Transaction tx = null;
-
-                    try {
-                        Method method = HibernateUtil.class.getDeclaredMethod("getSessionFactory");
-                        method.setAccessible(true);  // Bypass private access
-                        SessionFactory sessionFactory = (SessionFactory) method.invoke(hibernateUtil);
-
-                        session = sessionFactory.openSession();
-                        tx = session.beginTransaction();
-                        for (DrsObject object : batch) {
-                            try {
-                                session.save(object);
-                            } catch (HibernateException ex) {
-                                loggingUtil.error("HibernateException occurred: " + ex);
-                                failedBatch.add(object);
-                            }
-                        }
-                        session.flush();
-                        session.clear();
-                        tx.commit();
-                    } catch (Exception ex) {
-                        if (tx != null) {
-                            tx.rollback();
-                        }
-                        loggingUtil.error("Transaction rolled back due to: " + ex);
-                        throw ex;
-
-                    } finally {
-                        if (session != null && session.isOpen()) {
-                            session.close();
-                        }
-                    }
-                    return failedBatch;
-                }));
-            }
-
-            List<DrsObject> allFailedRecords = new ArrayList<>();
-            for (Future<List<DrsObject>> future : futures) {
-                allFailedRecords.addAll(future.get());
-            }
-            return allFailedRecords;
-        } finally {
-            executor.shutdown();
-        }
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/hibernate/package-info.java b/deprecated/starterkit/drs/utils/hibernate/package-info.java
deleted file mode 100644
index 83d0e9fa..00000000
--- a/deprecated/starterkit/drs/utils/hibernate/package-info.java
+++ /dev/null
@@ -1,5 +0,0 @@
-/**
- * Custom hibernate-related classes for facilitating access to DRS entities in
- * the database via hibernate API
- */
-package org.ga4gh.starterkit.drs.utils.hibernate;
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/utils/package-info.java b/deprecated/starterkit/drs/utils/package-info.java
deleted file mode 100644
index e9848811..00000000
--- a/deprecated/starterkit/drs/utils/package-info.java
+++ /dev/null
@@ -1,4 +0,0 @@
-/**
- * Helper/utility classes for various uses throughout the DRS service application 
- */
-package org.ga4gh.starterkit.drs.utils;
\ No newline at end of file
diff --git a/deprecated/starterkit/drs/utils/passport/UserPassport.java b/deprecated/starterkit/drs/utils/passport/UserPassport.java
deleted file mode 100644
index 167025a4..00000000
--- a/deprecated/starterkit/drs/utils/passport/UserPassport.java
+++ /dev/null
@@ -1,19 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.passport;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-public class UserPassport {
-
-    private String passportJwt;
-    private Map<String, String> visaJwtMap;
-
-    public UserPassport() {
-        visaJwtMap = new HashMap<>();
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/passport/UserPassportMap.java b/deprecated/starterkit/drs/utils/passport/UserPassportMap.java
deleted file mode 100644
index e6b6d28a..00000000
--- a/deprecated/starterkit/drs/utils/passport/UserPassportMap.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.passport;
-
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-import com.auth0.jwt.JWT;
-import com.auth0.jwt.interfaces.DecodedJWT;
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-public class UserPassportMap {
-
-    private Map<String, UserPassport> map;
-
-    public UserPassportMap(List<String> passports) {
-        map = new HashMap<>();
-
-        for (String rawPassportJwt : passports) {
-            UserPassport userPassport = new UserPassport();
-            userPassport.setPassportJwt(rawPassportJwt);
-
-            DecodedJWT decodedPassportJwt = JWT.decode(rawPassportJwt);
-            String passportIss = decodedPassportJwt.getClaim("iss").asString();
-            
-            String[] containedVisas = decodedPassportJwt.getClaim("contained_visas").asArray(String.class);
-            String[] rawVisaJwts = decodedPassportJwt.getClaim("ga4gh_passport_v1").asArray(String.class);
-            for (int i = 0; i < containedVisas.length; i++) {
-                String containedVisa = containedVisas[i];
-                String rawVisaJwt = rawVisaJwts[i];
-                userPassport.getVisaJwtMap().put(containedVisa, rawVisaJwt);
-            }
-            map.put(passportIss, userPassport);
-        }
-    }
-
-    public void verifyAllJwts() {
-
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/passport/UserPassportMapVerifier.java b/deprecated/starterkit/drs/utils/passport/UserPassportMapVerifier.java
deleted file mode 100644
index b7263046..00000000
--- a/deprecated/starterkit/drs/utils/passport/UserPassportMapVerifier.java
+++ /dev/null
@@ -1,67 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.passport;
-
-import com.auth0.jwt.JWT;
-import com.auth0.jwt.JWTVerifier;
-import com.auth0.jwt.algorithms.Algorithm;
-
-import org.ga4gh.starterkit.common.exception.BadRequestException;
-import org.ga4gh.starterkit.drs.exception.UnauthorizedException;
-import org.ga4gh.starterkit.drs.model.PassportBroker;
-import org.ga4gh.starterkit.drs.model.PassportVisa;
-import org.ga4gh.starterkit.drs.utils.hibernate.DrsHibernateUtil;
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lombok.Getter;
-import lombok.Setter;
-
-@Setter
-@Getter
-public class UserPassportMapVerifier {
-
-    @Autowired
-    private DrsHibernateUtil hibernateUtil;
-
-    @Autowired
-    private LoggingUtil loggingUtil;
-
-    public void verifyAll(UserPassportMap userPassportMap) {
-        try {
-            for (String passportIssKey : userPassportMap.getMap().keySet()) {
-                // verify the passport-level JWT
-                // first find the secret from the DB
-                // then use it to verify
-                UserPassport userPassport = userPassportMap.getMap().get(passportIssKey);
-                String rawPassportJwt = userPassport.getPassportJwt();
-                PassportBroker passportBroker = hibernateUtil.readEntityObject(PassportBroker.class, passportIssKey, false);
-                if (passportBroker == null) {
-                    String exceptionMessage = "Passports from issuer: '" + passportIssKey + "' are not accepted here.";
-                    loggingUtil.error("Exception occurred: passport broker is null " + exceptionMessage);
-                    throw new Exception(exceptionMessage);
-                }
-                String passportBrokerSecret = passportBroker.getSecret();
-                JWTVerifier passportVerifier = JWT.require(Algorithm.HMAC256(passportBrokerSecret)).build();
-                passportVerifier.verify(rawPassportJwt);
-
-                for (String visaKey : userPassport.getVisaJwtMap().keySet()) {
-                    String rawVisaJwt = userPassport.getVisaJwtMap().get(visaKey);
-                    String visaName = visaKey.split("@")[0];
-                    String visaIssuer = visaKey.split("@")[1];
-                    PassportVisa registeredVisa = hibernateUtil.findPassportVisa(visaName, visaIssuer);
-                    if (registeredVisa == null) {
-                        String exceptionMessage = "The Visa you provided: '" + visaKey + "' is not accepted here.";
-                        loggingUtil.error("Exception occurred: registered visa is null " + exceptionMessage);
-                        throw new Exception(exceptionMessage);
-                    }
-                    String visaSecret = registeredVisa.getSecret();
-                    JWTVerifier visaVerifier = JWT.require(Algorithm.HMAC256(visaSecret)).build();
-                    visaVerifier.verify(rawVisaJwt);
-                }
-            }
-        } catch (Exception ex) {
-            String message = "Invalid Passport(s), message: " + ex.getMessage();
-            loggingUtil.error("Exception occurred: " + message);
-            throw new UnauthorizedException(message);
-        }
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/requesthandler/AccessRequestHandler.java b/deprecated/starterkit/drs/utils/requesthandler/AccessRequestHandler.java
deleted file mode 100644
index a2ad63fe..00000000
--- a/deprecated/starterkit/drs/utils/requesthandler/AccessRequestHandler.java
+++ /dev/null
@@ -1,81 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.requesthandler;
-
-import java.net.URI;
-import org.ga4gh.starterkit.common.config.ServerProps;
-import static org.ga4gh.starterkit.drs.constant.DrsApiConstants.DRS_API_V1;
-import org.ga4gh.starterkit.common.exception.ResourceNotFoundException;
-import org.ga4gh.starterkit.common.requesthandler.RequestHandler;
-import org.ga4gh.starterkit.common.util.logging.LoggingUtil;
-import org.ga4gh.starterkit.drs.model.AccessURL;
-import org.ga4gh.starterkit.drs.utils.cache.AccessCache;
-import org.ga4gh.starterkit.drs.utils.cache.AccessCacheItem;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * Request handling logic for providing an AccessURL from a provided DrsObject id
- * and access ID
- */
-public class AccessRequestHandler implements RequestHandler<AccessURL> {
-
-    @Autowired
-    private ServerProps serverProps;
-
-    @Autowired
-    private AccessCache accessCache;
-
-    @Autowired
-    private LoggingUtil loggingUtil;
-
-    private String objectId;
-    private String accessId;
-
-    /**
-     * Instantiates a new AccessRequestHandler
-     */
-    public AccessRequestHandler() {
-
-    }
-
-    /**
-     * Prepares the request handler with input params from the controller function
-     * @param objectId DrsObject identifier
-     * @param accessId access identifier
-     * @return the prepared request handler
-     */
-    public AccessRequestHandler prepare(String objectId, String accessId) {
-        this.objectId = objectId;
-        this.accessId = accessId;
-        return this;
-    }
-
-    /**
-     * Provides an AccessURL for the given DrsObject id and access ID
-     */
-    public AccessURL handleRequest() {
-        AccessCacheItem cacheItem = accessCache.get(objectId, accessId);
-        if (cacheItem == null) {
-            String exceptionMessage = "invalid access_id/object_id " + accessId + '/' + objectId;
-            loggingUtil.error("Exception occurred: " + exceptionMessage);
-            throw new ResourceNotFoundException(exceptionMessage);
-        }
-
-        AccessURL accessURL = generateAccessURLForFile();
-        return accessURL;
-    }
-
-    /**
-     * Constructs the streaming endpoint URL for the given ids
-     * @return AccessURL pointing to this service's streaming endpoint
-     */
-    private AccessURL generateAccessURLForFile() {
-        String path = DRS_API_V1 + "/stream/" + objectId + "/" + accessId;
-
-        StringBuffer uriBuffer = new StringBuffer(serverProps.getScheme() + "://");
-        uriBuffer.append(serverProps.getHostname());
-        if (!serverProps.getPublicApiPort().equals("80")) {
-            uriBuffer.append(":" + serverProps.getPublicApiPort());
-        }
-        uriBuffer.append(path);
-        return new AccessURL(URI.create(uriBuffer.toString()));
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/requesthandler/AuthInfoRequestHandler.java b/deprecated/starterkit/drs/utils/requesthandler/AuthInfoRequestHandler.java
deleted file mode 100644
index 867ffe85..00000000
--- a/deprecated/starterkit/drs/utils/requesthandler/AuthInfoRequestHandler.java
+++ /dev/null
@@ -1,58 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.requesthandler;
-
-import org.ga4gh.starterkit.common.exception.ResourceNotFoundException;
-import org.ga4gh.starterkit.common.requesthandler.RequestHandler;
-import org.ga4gh.starterkit.drs.model.AuthInfo;
-import org.ga4gh.starterkit.drs.model.AuthIssuer;
-import org.ga4gh.starterkit.drs.model.AuthType;
-import org.ga4gh.starterkit.drs.model.DrsObject;
-import org.ga4gh.starterkit.drs.model.PassportVisa;
-import org.ga4gh.starterkit.drs.utils.hibernate.DrsHibernateUtil;
-import org.springframework.beans.factory.annotation.Autowired;
-
-import lombok.Getter;
-import lombok.NoArgsConstructor;
-import lombok.Setter;
-
-@Setter
-@Getter
-@NoArgsConstructor
-public class AuthInfoRequestHandler implements RequestHandler<AuthInfo> {
-    
-    @Autowired
-    private DrsHibernateUtil hibernateUtil;
-
-    private String objectId;
-
-    public AuthInfoRequestHandler prepare(String objectId) {
-        this.objectId = objectId;
-        return this;
-    }
-
-    public AuthInfo handleRequest() {
-        AuthInfo authInfo = new AuthInfo();
-
-        DrsObject drsObject = hibernateUtil.loadDrsObject(objectId, false);
-        if (drsObject == null) {
-            throw new ResourceNotFoundException("No DrsObject found by id: " + objectId);
-        }
-
-        if (drsObject.getPassportVisas().size() == 0) {
-            authInfo.getSupportedTypes().add(AuthType.None);
-        } else {
-            authInfo.getSupportedTypes().add(AuthType.PassportAuth);
-
-            for (PassportVisa visa : drsObject.getPassportVisas()) {
-                AuthIssuer issuer = new AuthIssuer();
-                issuer.setBrokerUrl(visa.getPassportBroker().getId());
-                issuer.setVisaName(visa.getName());
-                issuer.setVisaIssuer(visa.getIssuer());
-                authInfo.getPassportAuthIssuers().add(issuer);
-            }
-        }
-        System.out.println("what is auth info??");
-        System.out.println(authInfo.getSupportedTypes().size());
-        System.out.println(authInfo.getSupportedTypes().get(0));
-        return authInfo;
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/requesthandler/FileStreamRequestHandler.java b/deprecated/starterkit/drs/utils/requesthandler/FileStreamRequestHandler.java
deleted file mode 100644
index aebfb329..00000000
--- a/deprecated/starterkit/drs/utils/requesthandler/FileStreamRequestHandler.java
+++ /dev/null
@@ -1,74 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.requesthandler;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.IOException;
-import java.io.InputStream;
-import javax.servlet.http.HttpServletResponse;
-import org.apache.commons.io.IOUtils;
-import org.ga4gh.starterkit.common.exception.ResourceNotFoundException;
-import org.ga4gh.starterkit.common.requesthandler.RequestHandler;
-import org.ga4gh.starterkit.drs.utils.cache.AccessCache;
-import org.ga4gh.starterkit.drs.utils.cache.AccessCacheItem;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * Enables handling logic for the streaming endpoint, allows files stored on the 
- * service's file system to be streamed over the API
- */
-public class FileStreamRequestHandler implements RequestHandler<Void> {
-
-    @Autowired
-    private AccessCache accessCache;
-
-    private String objectId;
-    private String accessId;
-    private HttpServletResponse response;
-
-    /**
-     * Prepares the request handler with input params from the controller function
-     * @param objectId DrsObject identifier
-     * @param accessId access identifier
-     * @param response low-level Spring response object handling file streaming
-     * @return the prepared request handler
-     */
-    public FileStreamRequestHandler prepare(String objectId, String accessId, HttpServletResponse response) {
-        this.objectId = objectId;
-        this.accessId = accessId;
-        this.response = response;
-        return this;
-    }
-
-    /**
-     * Streams the file contents referenced by the provided object id and access id
-     * to client
-     */
-    public Void handleRequest() {
-        // look up the access cache to see if a valid set of object id and 
-        // access id was provided
-        AccessCacheItem cacheItem = accessCache.get(objectId, accessId);
-        if (cacheItem == null) {
-            throw new ResourceNotFoundException("invalid access_id/object_id");
-        }
-
-        try {
-            // Open file input stream
-            InputStream inputStream = new FileInputStream(new File(cacheItem.getObjectPath()));
-
-            // Set Response headers
-            response.addHeader("Content-Disposition", "attachment");
-            if (cacheItem.getMimeType() != null) {
-                response.setContentType(cacheItem.getMimeType());
-            }
-
-            // copy file input stream to response's output stream
-            IOUtils.copy(inputStream, response.getOutputStream());
-            response.flushBuffer();
-        } catch (IOException e) {
-            // TODO THROW REST CONTROLLER EXCEPTION
-            return null;
-        }
-
-        return null;
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/requesthandler/ObjectRequestHandler.java b/deprecated/starterkit/drs/utils/requesthandler/ObjectRequestHandler.java
deleted file mode 100644
index b411d557..00000000
--- a/deprecated/starterkit/drs/utils/requesthandler/ObjectRequestHandler.java
+++ /dev/null
@@ -1,284 +0,0 @@
-package org.ga4gh.starterkit.drs.utils.requesthandler;
-
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.List;
-import java.util.UUID;
-import org.ga4gh.starterkit.common.config.ServerProps;
-import org.ga4gh.starterkit.common.exception.ResourceNotFoundException;
-import org.ga4gh.starterkit.common.requesthandler.RequestHandler;
-import org.ga4gh.starterkit.drs.config.DrsServiceProps;
-import org.ga4gh.starterkit.drs.exception.ForbiddenException;
-import org.ga4gh.starterkit.drs.exception.UnauthorizedException;
-import org.ga4gh.starterkit.drs.model.AccessMethod;
-import org.ga4gh.starterkit.drs.model.AccessType;
-import org.ga4gh.starterkit.drs.model.AccessURL;
-import org.ga4gh.starterkit.drs.model.AwsS3AccessObject;
-import org.ga4gh.starterkit.drs.model.ContentsObject;
-import org.ga4gh.starterkit.drs.model.DrsObject;
-import org.ga4gh.starterkit.drs.model.FileAccessObject;
-import org.ga4gh.starterkit.drs.model.PassportVisa;
-import org.ga4gh.starterkit.drs.utils.cache.AccessCache;
-import org.ga4gh.starterkit.drs.utils.cache.AccessCacheItem;
-import org.ga4gh.starterkit.drs.utils.hibernate.DrsHibernateUtil;
-import org.ga4gh.starterkit.drs.utils.passport.UserPassport;
-import org.ga4gh.starterkit.drs.utils.passport.UserPassportMap;
-import org.springframework.beans.factory.annotation.Autowired;
-
-/**
- * Request handling logic for loading a DRSObject and formatting it according
- * to the DRS specification
- */
-public class ObjectRequestHandler implements RequestHandler<DrsObject> {
-
-    @Autowired
-    ServerProps serverProps;
-
-    @Autowired
-    DrsServiceProps drsServiceProps;
-
-    @Autowired
-    AccessCache accessCache;
-
-    @Autowired
-    DrsHibernateUtil hibernateUtil;
-
-    private String objectId;
-
-    private boolean expand;
-
-    private UserPassportMap userPassportMap;
-
-    /* Constructors */
-
-    /**
-     * Instantiate a new ObjectRequestHandler
-     */
-    public ObjectRequestHandler() {
-        
-    }
-
-    /**
-     * Prepares the request handler with input params from the controller function
-     * @param objectId DrsObject identifier
-     * @param expand boolean indicating whether to return nested/recursive bundles under 'contents'
-     * @return the prepared request handler
-     */
-    public ObjectRequestHandler prepare(String objectId, boolean expand, UserPassportMap userPassportMap) {
-        this.objectId = objectId;
-        this.expand = expand;
-        this.userPassportMap = userPassportMap;
-        return this;
-    }
-
-    /**
-     * Obtains information about a DRSObject and formats it to the DRS specification
-     */
-    public DrsObject handleRequest() {
-        // Get DrsObject from db
-        DrsObject drsObject = hibernateUtil.loadDrsObject(objectId, true);
-        if (drsObject == null) {
-            throw new ResourceNotFoundException("No DrsObject found by id: " + objectId);
-        }
-
-        // check if DrsObject requires auth, if so verify the client's passport
-        List<PassportVisa> requiredVisas = drsObject.getPassportVisas();
-        boolean requiresAuth = false;
-        if (requiredVisas != null && requiredVisas.size() > 0) {
-            requiresAuth = true;
-        }
-        boolean noPassport = userPassportMap == null || userPassportMap.getMap().size() == 0;
-        if (requiresAuth) {
-            if (noPassport) {
-                throw new UnauthorizedException("Request for controlled data is missing user passport(s)");
-            }
-
-            // need to verify at least 1 visa registered with the DRS Object
-            boolean matchingVisaFound = false;
-            for (PassportVisa drsObjectRegisteredVisa : drsObject.getPassportVisas()) {
-                String passportBrokerIss = drsObjectRegisteredVisa.getPassportBroker().getUrl();
-                String visaName = drsObjectRegisteredVisa.getName();
-                String visaIssuer = drsObjectRegisteredVisa.getIssuer();
-                UserPassport userPassport = userPassportMap.getMap().get(passportBrokerIss);
-                if (userPassport != null) {
-                    String visaKey = visaName + "@" + visaIssuer;
-                    String visaJwt = userPassport.getVisaJwtMap().get(visaKey);
-                    if (visaJwt != null)  {
-                        matchingVisaFound = true;
-                    }
-                }
-            }
-
-            if (! matchingVisaFound) {
-                throw new ForbiddenException("No suitable visa found in user passport(s) for requested DRS object");
-            }
-        }
-
-        // post query prep of response
-        drsObject.setSelfURI(prepareSelfURI(objectId));
-        drsObject.setContents(prepareContents(drsObject));
-        drsObject.setAccessMethods(prepareAccessMethods(drsObject));
-        return drsObject;
-    }
-
-    /**
-     * Constructs the self URI from server hostname and object id
-     * @param id DrsObject identifier
-     * @return self-referencing URI
-     */
-    private URI prepareSelfURI(String id) {
-        StringBuffer uriBuffer = new StringBuffer("drs://");
-        uriBuffer.append(serverProps.getHostname());
-        if (!serverProps.getPublicApiPort().equals("80")) {
-            uriBuffer.append(":" + serverProps.getPublicApiPort());
-        }
-        uriBuffer.append("/" + id.toString());
-        return URI.create(uriBuffer.toString());
-    }
-
-    /**
-     * Constructs the contents object list from a DrsObject's children
-     * @param drsObject DrsObject with loaded children
-     * @return List of contents objects derived from children
-     */
-    private List<ContentsObject> prepareContents(DrsObject drsObject) {
-        List<ContentsObject> contents = new ArrayList<>();
-        for (int i = 0; i < drsObject.getDrsObjectChildren().size(); i++) {
-            contents.add(createContentsObject(drsObject.getDrsObjectChildren().get(i)));
-        }
-        return contents;
-    }
-
-    /**
-     * Constructs a single contents object from a DrsObject
-     * @param drsObject DrsObject to be converted into a ContentsObject
-     * @return ContentsObject derived from the DrsObject
-     */
-    private ContentsObject createContentsObject(DrsObject drsObject) {
-        ContentsObject contentsObject = new ContentsObject();
-        contentsObject.setId(drsObject.getId());
-        contentsObject.setDrsUri(new ArrayList<URI>(){{
-            add(prepareSelfURI(drsObject.getId()));
-        }});
-        contentsObject.setName(drsObject.getName());
-
-        // if 'expand' boolean is true, perform recursive function to recursively
-        // convert all children DrsObjects to ContentsObjects
-        if (expand) {
-            List<ContentsObject> childContents = new ArrayList<>();
-            for (int i = 0; i < drsObject.getDrsObjectChildren().size(); i++) {
-                childContents.add(createContentsObject(drsObject.getDrsObjectChildren().get(i)));
-            }
-            contentsObject.setContents(childContents);
-        }
-        
-        return contentsObject;
-    }
-
-    /**
-     * Constructs a combined list of access methods from all different types
-     * of AccessObjects (eg FileAccessObjects, AwsS3AccessObjects)
-     * @param drsObject the DrsObject for which the access methods list will be constructed
-     * @return list of access methods
-     */
-    private List<AccessMethod> prepareAccessMethods(DrsObject drsObject) {
-
-        List<AccessMethod> accessMethods = new ArrayList<>();
-
-        // Convert file-based access objects to AccessMethods
-        // if indicated by the DrsServiceProps, return a 'file://' URL indicating
-        // the direct path and/or an 'http(s)://' URL pointing to the streaming
-        // endpoint
-        for (FileAccessObject fileAccessObject : drsObject.getFileAccessObjects()) {
-            if (drsServiceProps.getServeFileURLForFileObjects()) {
-                accessMethods.add(createFileURLAccessMethodForFileObject(fileAccessObject));
-            }
-            if (drsServiceProps.getServeStreamURLForFileObjects()) {
-                accessMethods.add(createStreamAccessMethodForFileObject(fileAccessObject));
-            }
-        }
-
-        // Convert s3-based access objects to AccessMethods
-        for (AwsS3AccessObject awsS3AccessObject : drsObject.getAwsS3AccessObjects()) {
-            accessMethods.add(createAccessMethod(awsS3AccessObject));
-        }
-        
-        return accessMethods;
-    }
-
-    /**
-     * Construct a file:// URL for a file-based access object
-     * @param fileAccessObject file-based access object
-     * @return access method with a file:// URL
-     */
-    private AccessMethod createFileURLAccessMethodForFileObject(FileAccessObject fileAccessObject) {
-        AccessMethod accessMethod = new AccessMethod();
-        accessMethod.setType(AccessType.file);
-        AccessURL accessURL = new AccessURL(URI.create(
-            "file://" + fileAccessObject.getPath()
-        ));
-        accessMethod.setAccessUrl(accessURL);
-        return accessMethod;
-    }
-
-    /**
-     * Construct an http(s):// URL pointing to streaming endpoint for a file-based access object
-     * @param fileAccessObject file-based access object
-     * @return access method with a http(s):// URL
-     */
-    private AccessMethod createStreamAccessMethodForFileObject(FileAccessObject fileAccessObject) {
-        AccessMethod accessMethod = new AccessMethod();
-        accessMethod.setType(AccessType.https);
-
-        // populate the cache with a new item containing the access ID so it
-        // can be recgonized by the access endpoint
-        String accessID = UUID.randomUUID().toString();
-        AccessCacheItem accessCacheItem = generateAccessCacheItem(
-            fileAccessObject.getDrsObject().getId(),
-            accessMethod.getAccessId(),
-            fileAccessObject.getPath(),
-            accessMethod.getType(),
-            fileAccessObject.getDrsObject().getMimeType());
-        accessCache.put(fileAccessObject.getDrsObject().getId(), accessID, accessCacheItem);
-
-        accessMethod.setAccessId(accessID);
-        return accessMethod;
-    }
-
-    /**
-     * Construct an s3:// URL for an s3-based access object
-     * @param awsS3AccessObject S3-based access object
-     * @return access method with s3:// URL
-     */
-    private AccessMethod createAccessMethod(AwsS3AccessObject awsS3AccessObject) {
-        AccessMethod accessMethod = new AccessMethod();
-        accessMethod.setType(AccessType.s3);
-        accessMethod.setRegion(awsS3AccessObject.getRegion());
-
-        AccessURL accessURL = new AccessURL(URI.create(
-            "s3://" + awsS3AccessObject.getBucket() 
-            + awsS3AccessObject.getKey()));
-        accessMethod.setAccessUrl(accessURL);
-        return accessMethod;
-
-    }
-
-    /**
-     * Create an access cache item with the supplied parameters
-     * @param objectId DrsObject identifier
-     * @param accessId access id
-     * @param objectPath file path/URL to byte source 
-     * @param accessType path/URL type
-     * @param mimeType media type
-     * @return access cache item populated with the supplied parameters
-     */
-    private AccessCacheItem generateAccessCacheItem(String objectId, String accessId, String objectPath, AccessType accessType, String mimeType) {
-        AccessCacheItem item = new AccessCacheItem();
-        item.setObjectId(objectId);
-        item.setAccessId(accessId);
-        item.setObjectPath(objectPath);
-        item.setAccessType(accessType);
-        item.setMimeType(mimeType);
-        return item;
-    }
-}
diff --git a/deprecated/starterkit/drs/utils/requesthandler/package-info.java b/deprecated/starterkit/drs/utils/requesthandler/package-info.java
deleted file mode 100644
index 60900de9..00000000
--- a/deprecated/starterkit/drs/utils/requesthandler/package-info.java
+++ /dev/null
@@ -1,6 +0,0 @@
-/**
- * Contains classes that harbor the main logic for controller functions,
- * abstracting it away from the 'controller' package. Request handlers are
- * ephemeral and loaded on a per-request basis
- */
-package org.ga4gh.starterkit.drs.utils.requesthandler;
\ No newline at end of file
diff --git a/liquibase/dbchangelog.xml b/liquibase/dbchangelog.xml
index 5ca1d12a..65460e43 100644
--- a/liquibase/dbchangelog.xml
+++ b/liquibase/dbchangelog.xml
@@ -169,4 +169,14 @@
     <changeSet author="jadams" id="fkconstraint-tb-passport-user-visa-assertion-column-visa-id-refs-passport-visa">
         <addForeignKeyConstraint baseColumnNames="visa_id" baseTableName="passport_user_visa_assertion" constraintName="passport_user_visa_assertion_visa_id_fkey" deferrable="false" initiallyDeferred="false" onDelete="CASCADE" onUpdate="NO ACTION" referencedColumnNames="id" referencedTableName="passport_visa" validate="true"/>
     </changeSet>
+    <changeSet author="jadams" id="add-manifest-columns-to-drs-objects">
+        <addColumn tableName="drs_object">
+            <column name="is_manifest" type="boolean" defaultValueBoolean="false">
+                <constraints nullable="false"/>
+            </column>
+            <column name="manifest_content" type="jsonb">
+                <constraints nullable="true"/>
+            </column>
+        </addColumn>
+    </changeSet>
 </databaseChangeLog>
diff --git a/src/main/java/org/ga4gh/refcloud/api/core/dataset/DatasetPublicController.java b/src/main/java/org/ga4gh/refcloud/api/core/dataset/DatasetPublicController.java
index a4155628..cd92d336 100644
--- a/src/main/java/org/ga4gh/refcloud/api/core/dataset/DatasetPublicController.java
+++ b/src/main/java/org/ga4gh/refcloud/api/core/dataset/DatasetPublicController.java
@@ -1,11 +1,14 @@
 package org.ga4gh.refcloud.api.core.dataset;
 
+import org.springframework.data.domain.Page;
 import org.springframework.http.ResponseEntity;
+import org.springframework.security.access.prepost.PreAuthorize;
 import org.springframework.security.core.annotation.AuthenticationPrincipal;
 import org.springframework.web.bind.annotation.*;
 import java.util.List;
+
+import org.ga4gh.refcloud.api.drs.drsobject.DrsObject;
 import org.ga4gh.refcloud.api.security.KratosSessionResponse.Identity;
-import org.springframework.web.bind.annotation.PostMapping;
 
 @RestController
 @RequestMapping("/datasets")
@@ -34,4 +37,17 @@ public ResponseEntity<DatasetResponseDTO> requestAccessToDatasetById(@Authentica
         DatasetResponseDTO dataset = datasetService.requestAccessToDatasetById(identity.getId(), datasetId);
         return ResponseEntity.ok(dataset);
     }
+
+    @GetMapping("/{datasetId}/manifests")
+    @PreAuthorize("@GA4GHPassportTokenEvaluator.canAccessDataset(authentication, #datasetId)")
+    public ResponseEntity<Page<ManifestResponseDTO>> getManifestsForDataset(
+        @PathVariable String datasetId,
+        @RequestParam(defaultValue = "0") int page,
+        @RequestParam(defaultValue = "10") int size,
+        @RequestParam(defaultValue = "id") String sortBy,
+        @RequestParam(defaultValue = "asc") String direction
+    ) {
+        Page<ManifestResponseDTO> manifestDtoPage = datasetService.getDrsObjectManifestsForDataset(datasetId, page, size, sortBy, direction);
+        return ResponseEntity.ok(manifestDtoPage);
+    }
 }
diff --git a/src/main/java/org/ga4gh/refcloud/api/core/dataset/DatasetService.java b/src/main/java/org/ga4gh/refcloud/api/core/dataset/DatasetService.java
index 98037993..ab61ea76 100644
--- a/src/main/java/org/ga4gh/refcloud/api/core/dataset/DatasetService.java
+++ b/src/main/java/org/ga4gh/refcloud/api/core/dataset/DatasetService.java
@@ -1,13 +1,22 @@
 package org.ga4gh.refcloud.api.core.dataset;
 
 import org.ga4gh.refcloud.api.core.tag.Tag;
+import org.ga4gh.refcloud.api.drs.drsobject.DrsObject;
+import org.ga4gh.refcloud.api.drs.drsobject.DrsObjectRepository;
+import org.ga4gh.refcloud.api.drs.drsobject.DrsObjectService;
+import org.ga4gh.refcloud.api.exception.ResourceNotFoundException;
 import org.ga4gh.refcloud.api.passport.passportuser.PassportUser;
 import org.ga4gh.refcloud.api.passport.passportuser.PassportUserRepository;
 import org.ga4gh.refcloud.api.passport.passportuservisaassertion.PassportUserVisaAssertion;
 import org.ga4gh.refcloud.api.passport.passportuservisaassertion.PassportUserVisaAssertionRepository;
 import org.ga4gh.refcloud.api.passport.passportuservisaassertion.PassportUserVisaAssertionResponseDTO;
+import org.ga4gh.refcloud.api.passport.passportuservisaassertion.PassportUserVisaAssertionService;
 import org.ga4gh.refcloud.api.passport.passportuservisaassertion.PassportVisaAssertionStatus;
 import org.ga4gh.refcloud.api.passport.passportvisa.PassportVisaResponseDTO;
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.PageRequest;
+import org.springframework.data.domain.Pageable;
+import org.springframework.data.domain.Sort;
 import org.springframework.stereotype.Service;
 import org.springframework.transaction.annotation.Transactional;
 import java.time.LocalDateTime;
@@ -23,14 +32,20 @@ public class DatasetService {
 
     private final DatasetRepository datasetRepository;
 
+    private final PassportUserVisaAssertionService passportUserVisaAssertionService;
+
     private final PassportUserRepository passportUserRepository;
 
     private final PassportUserVisaAssertionRepository passportUserVisaAssertionRepository;
 
-    public DatasetService(DatasetRepository datasetRepository, PassportUserRepository passportUserRepository, PassportUserVisaAssertionRepository passportUserVisaAssertionRepository) {
+    private final DrsObjectRepository drsObjectRepository;
+
+    public DatasetService(DatasetRepository datasetRepository, PassportUserVisaAssertionService passportUserVisaAssertionService, PassportUserRepository passportUserRepository, PassportUserVisaAssertionRepository passportUserVisaAssertionRepository, DrsObjectRepository drsObjectRepository) {
         this.datasetRepository = datasetRepository;
+        this.passportUserVisaAssertionService = passportUserVisaAssertionService;
         this.passportUserRepository = passportUserRepository;
         this.passportUserVisaAssertionRepository = passportUserVisaAssertionRepository;
+        this.drsObjectRepository = drsObjectRepository;
     }
 
     @Transactional(readOnly = true)
@@ -79,6 +94,12 @@ public DatasetResponseDTO getDatasetById(String userId, String datasetId) {
         return convertToResponseDto(dataset, assertion);
     }
 
+    @Transactional(readOnly = true)
+    public String getVisaIdByDatasetId(String id) {
+        Dataset dataset = loadDataset(id);
+        return dataset.getPassportVisa().getId();
+    }
+
     @Transactional
     public DatasetResponseDTO requestAccessToDatasetById(String userId, String datasetId) {
         // retrieve dataset & visa object from db
@@ -109,6 +130,45 @@ public DatasetResponseDTO requestAccessToDatasetById(String userId, String datas
         return convertToResponseDto(dataset, assertion);
     }
 
+    @Transactional
+    public Page<ManifestResponseDTO> getDrsObjectManifestsForDataset(String datasetId, int page, int size, String sortBy, String direction) {
+        Sort sort = direction.equalsIgnoreCase("desc") ?
+                    Sort.by(sortBy).descending() :
+                    Sort.by(sortBy).ascending();
+        Pageable pageable = PageRequest.of(page, size, sort);
+        Page<DrsObject> drsObjectsPage = drsObjectRepository.findDrsObjectManifestsByDatasetId(datasetId, pageable);
+        Page<ManifestResponseDTO> manifestDtoPage = drsObjectsPage.map(drsObject -> new ManifestResponseDTO(
+            drsObject.getId(),
+            drsObject.getName(),
+            drsObject.getSize(),
+            drsObject.getCreatedTime(),
+            drsObject.getUpdatedTime(),
+            drsObject.getVersion(),
+            drsObject.getMimeType(),
+            drsObject.getDescription(),
+            drsObject.getIsManifest(),
+            drsObject.getManifestContent()
+        ));
+        return manifestDtoPage;
+    }
+
+    public boolean validateUserIsAuthorizedForDataset(String userId, String datasetId) {
+        String visaId = getVisaIdByDatasetId(datasetId);
+        Optional<PassportUserVisaAssertion> optionalAssertion = passportUserVisaAssertionService.getAssertionByUserIdAndVisaId(userId, visaId);
+        if (optionalAssertion.isPresent()) {
+            PassportUserVisaAssertion assertion = optionalAssertion.get();
+            if (assertion.getCurrentStatus() == PassportVisaAssertionStatus.Approved) {
+                return true; // if status is "Approved" allow user to view the object
+            }
+        }
+
+        return false; // do not allow user to view the object if no record found in assertion table, or if status is anything other than "Approved"
+    }
+
+    private Dataset loadDataset(String id) {
+        return datasetRepository.findByIdWithTagsAndVisas(id).orElseThrow(() -> new ResourceNotFoundException("No Dataset with ID: " + id));
+    }
+
     private DatasetResponseDTO convertToResponseDto(Dataset dataset, PassportUserVisaAssertion assertion) {
         // prepare tags
         Set<String> tagDtos = dataset.getTags()
diff --git a/src/main/java/org/ga4gh/refcloud/api/core/dataset/ManifestResponseDTO.java b/src/main/java/org/ga4gh/refcloud/api/core/dataset/ManifestResponseDTO.java
new file mode 100644
index 00000000..e4e51a4b
--- /dev/null
+++ b/src/main/java/org/ga4gh/refcloud/api/core/dataset/ManifestResponseDTO.java
@@ -0,0 +1,20 @@
+package org.ga4gh.refcloud.api.core.dataset;
+
+import java.time.LocalDateTime;
+import java.util.Map;
+import tools.jackson.databind.PropertyNamingStrategies;
+import tools.jackson.databind.annotation.JsonNaming;
+
+@JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
+public record ManifestResponseDTO(
+    String id,
+    String name,
+    Long size,
+    LocalDateTime created,
+    LocalDateTime updated,
+    String version,
+    String mimeType,
+    String description,
+    Boolean isManifest,
+    Map<String, Object> manifestContent
+) {}
diff --git a/src/main/java/org/ga4gh/refcloud/api/drs/DrsConfig.java b/src/main/java/org/ga4gh/refcloud/api/drs/DrsConfig.java
index 14697eed..a690adde 100644
--- a/src/main/java/org/ga4gh/refcloud/api/drs/DrsConfig.java
+++ b/src/main/java/org/ga4gh/refcloud/api/drs/DrsConfig.java
@@ -5,6 +5,7 @@
 
 @ConfigurationProperties(prefix = "ga4gh.refcloud.drs")
 public record DrsConfig(
+    String scheme,
     String hostDomain,
     ServiceInfo serviceInfo
 ){
diff --git a/src/main/java/org/ga4gh/refcloud/api/drs/accessmethod/AccessMethodResponseDTO.java b/src/main/java/org/ga4gh/refcloud/api/drs/accessmethod/AccessMethodResponseDTO.java
index 6290df58..820b8cc8 100644
--- a/src/main/java/org/ga4gh/refcloud/api/drs/accessmethod/AccessMethodResponseDTO.java
+++ b/src/main/java/org/ga4gh/refcloud/api/drs/accessmethod/AccessMethodResponseDTO.java
@@ -1,12 +1,15 @@
 package org.ga4gh.refcloud.api.drs.accessmethod;
 
+import com.fasterxml.jackson.annotation.JsonInclude;
+
 import tools.jackson.databind.PropertyNamingStrategies;
 import tools.jackson.databind.annotation.JsonNaming;
 
 @JsonNaming(PropertyNamingStrategies.SnakeCaseStrategy.class)
+@JsonInclude(JsonInclude.Include.NON_NULL)
 public record AccessMethodResponseDTO(
     AccessMethodType type,
-    String accessUrl,
+    AccessUrlResponseDTO accessUrl,
     String cloud,
     String region,
     boolean available
diff --git a/src/main/java/org/ga4gh/refcloud/api/drs/accessmethod/AccessUrlResponseDTO.java b/src/main/java/org/ga4gh/refcloud/api/drs/accessmethod/AccessUrlResponseDTO.java
new file mode 100644
index 00000000..88ae1f19
--- /dev/null
+++ b/src/main/java/org/ga4gh/refcloud/api/drs/accessmethod/AccessUrlResponseDTO.java
@@ -0,0 +1,11 @@
+package org.ga4gh.refcloud.api.drs.accessmethod;
+
+import java.util.List;
+
+import com.fasterxml.jackson.annotation.JsonInclude;
+
+@JsonInclude(JsonInclude.Include.NON_NULL)
+public record AccessUrlResponseDTO(
+    String url,
+    List<String> headers
+) {}
diff --git a/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObject.java b/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObject.java
index a757254c..d63c2be8 100644
--- a/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObject.java
+++ b/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObject.java
@@ -2,12 +2,16 @@
 
 import java.time.LocalDateTime;
 import java.util.HashSet;
+import java.util.Map;
 import java.util.Set;
 import org.ga4gh.refcloud.api.core.dataset.Dataset;
 import org.ga4gh.refcloud.api.drs.awss3accessobject.AwsS3AccessObject;
 import org.ga4gh.refcloud.api.drs.drsobjectalias.DrsObjectAlias;
 import org.ga4gh.refcloud.api.drs.drsobjectchecksum.DrsObjectChecksum;
+import org.hibernate.annotations.JdbcTypeCode;
+import org.hibernate.type.SqlTypes;
 import jakarta.persistence.CascadeType;
+import jakarta.persistence.Column;
 import jakarta.persistence.Entity;
 import jakarta.persistence.FetchType;
 import jakarta.persistence.Id;
@@ -20,6 +24,7 @@
 import lombok.Getter;
 import lombok.NoArgsConstructor;
 import lombok.Setter;
+import tools.jackson.databind.JsonNode;
 
 @Entity
 @Table(name = "drs_object")
@@ -47,6 +52,12 @@ public class DrsObject {
 
     private String description;
 
+    private Boolean isManifest;
+
+    @JdbcTypeCode(SqlTypes.JSON)
+    @Column(name = "manifest_content", columnDefinition = "jsonb")
+    private Map<String, Object> manifestContent;
+
     @ManyToOne(fetch = FetchType.LAZY)
     @JoinColumn(name = "dataset_id", nullable = false) 
     private Dataset dataset;
diff --git a/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectPublicController.java b/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectPublicController.java
index 50a32fbf..f81f82b0 100644
--- a/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectPublicController.java
+++ b/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectPublicController.java
@@ -1,5 +1,7 @@
 package org.ga4gh.refcloud.api.drs.drsobject;
 
+import java.util.Map;
+
 import org.ga4gh.refcloud.api.drs.authinfo.MultiDrsObjectAuthInfoRequestDTO;
 import org.ga4gh.refcloud.api.drs.authinfo.MultiDrsObjectAuthInfoResponseDTO;
 import org.ga4gh.refcloud.api.drs.authinfo.MultiDrsObjectRequestDTO;
@@ -45,8 +47,8 @@ public ResponseEntity<DrsObjectResponseDTO> getDrsObjectByIdPostMethod(@PathVari
         return ResponseEntity.ok(drsObjectService.getDrsObjectById(id));
     }
 
-    @PreAuthorize("@GA4GHPassportTokenEvaluator.validateBulkAuthInfoRequest(authentication, #requestBody)")
     @RequestMapping(method=RequestMethod.OPTIONS)
+    @PreAuthorize("@GA4GHPassportTokenEvaluator.validateBulkAuthInfoRequest(authentication, #requestBody)")
     public ResponseEntity<MultiDrsObjectAuthInfoResponseDTO> getMultipleDrsObjectsAuthInfo(@Valid @RequestBody MultiDrsObjectAuthInfoRequestDTO requestBody) {
         return ResponseEntity.ok(drsObjectService.getMultiDrsObjectsAuthInfo(requestBody.bulkObjectIds()));
     }
@@ -56,4 +58,11 @@ public ResponseEntity<MultiDrsObjectAuthInfoResponseDTO> getMultipleDrsObjectsAu
     public ResponseEntity<MultiDrsObjectResponseDTO> getMultipleDrsObjects(@Valid @RequestBody MultiDrsObjectRequestDTO requestBody) {
         return ResponseEntity.ok(drsObjectService.getMultiDrsObjects(requestBody.passports(), requestBody.bulkObjectIds()));
     }
+
+    @GetMapping("/{id}/manifest-content")
+    @PreAuthorize("@GA4GHPassportTokenEvaluator.canAccessDrsObject(authentication, #id)")
+    public ResponseEntity<Map<String, Object>> getDrsObjectManifestContent(@PathVariable String id) {
+        Map<String, Object> manifestContent = drsObjectService.getDrsObjectManifestContent(id);
+        return ResponseEntity.ok(manifestContent);
+    }
 }
diff --git a/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectRepository.java b/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectRepository.java
index f5bc583a..d870bf9d 100644
--- a/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectRepository.java
+++ b/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectRepository.java
@@ -1,9 +1,16 @@
 package org.ga4gh.refcloud.api.drs.drsobject;
 
+import org.springframework.data.domain.Page;
+import org.springframework.data.domain.Pageable;
 import org.springframework.data.jpa.repository.JpaRepository;
+import org.springframework.data.jpa.repository.Query;
+import org.springframework.data.repository.query.Param;
 import org.springframework.stereotype.Repository;
 
 @Repository
 public interface DrsObjectRepository extends JpaRepository<DrsObject, String> {
 
+    @Query("SELECT d FROM DrsObject d WHERE d.dataset.id = :datasetId AND d.isManifest = true")
+    Page<DrsObject> findDrsObjectManifestsByDatasetId(@Param("datasetId") String datasetId, Pageable pageable);
+
 }
diff --git a/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectService.java b/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectService.java
index 65d7af6d..d6996b89 100644
--- a/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectService.java
+++ b/src/main/java/org/ga4gh/refcloud/api/drs/drsobject/DrsObjectService.java
@@ -2,12 +2,14 @@
 
 import java.util.ArrayList;
 import java.util.List;
+import java.util.Map;
 import java.util.Optional;
 import java.util.Set;
 import java.util.stream.Collectors;
 import org.ga4gh.refcloud.api.drs.DrsConfig;
 import org.ga4gh.refcloud.api.drs.accessmethod.AccessMethodResponseDTO;
 import org.ga4gh.refcloud.api.drs.accessmethod.AccessMethodType;
+import org.ga4gh.refcloud.api.drs.accessmethod.AccessUrlResponseDTO;
 import org.ga4gh.refcloud.api.drs.authinfo.MultiDrsObjectAuthInfoResponseDTO;
 import org.ga4gh.refcloud.api.drs.authinfo.MultiDrsObjectAuthInfoSummaryResponseDTO;
 import org.ga4gh.refcloud.api.drs.authinfo.MultiDrsObjectAuthInfoUnresolvedIdSetResponseDTO;
@@ -176,6 +178,15 @@ public boolean bulkRequestWithinLimit(List<String> bulkObjectIds) {
         return bulkObjectIds.size() <= drsConfig.serviceInfo().drs().maxBulkLengthRequest();
     }
 
+    @Transactional(readOnly = true)
+    public Map<String, Object> getDrsObjectManifestContent(String drsObjectId) {
+        DrsObject drsObject = loadDrsObject(drsObjectId);
+        if (!drsObject.getIsManifest()) {
+            throw new ResourceNotFoundException("DRS Object with ID: " + drsObjectId + " is not a manifest");
+        }
+        return drsObject.getManifestContent();
+    }
+
     @Transactional(readOnly = true)
     private Boolean requireDrsObjectExists(String id) {
         boolean exists = drsObjectRepository.existsById(id);
@@ -196,16 +207,38 @@ private DrsObjectResponseDTO convertToResponseDTO(DrsObject drsObject) {
             .map(checksum -> new DrsObjectChecksumResponseDTO(checksum.getChecksum(), checksum.getType()))
             .collect(Collectors.toSet());
 
-        Set<AccessMethodResponseDTO> accessMethodDtos = drsObject.getAwsS3AccessObjects()
+        Set<AccessMethodResponseDTO> accessMethodDtos;
+
+        if (drsObject.getIsManifest() == true) { // manifests - raw content stored as JSON in DB
+
+            accessMethodDtos = null;
+            accessMethodDtos = Set.of(
+                new AccessMethodResponseDTO(
+                    AccessMethodType.https,
+                    new AccessUrlResponseDTO(
+                        generateAccessUrlForManifestObject(drsObject.getId()),
+                        null
+                    ),
+                    null,
+                    null,
+                    true
+                )
+            );
+        } else { // AWS objects - raw content stored in S3
+            accessMethodDtos = drsObject.getAwsS3AccessObjects()
             .stream()
             .map(s3Object -> new AccessMethodResponseDTO(
                 AccessMethodType.https,
-                generateAccessUrlForOpenAccessS3Object(s3Object),
+                new AccessUrlResponseDTO(
+                    generateAccessUrlForOpenAccessS3Object(s3Object),
+                    null
+                ),
                 "aws",
                 s3Object.getRegion(),
                 true
             ))
             .collect(Collectors.toSet());
+        }
 
         Set<String> aliasDtos = drsObject.getAliases()
                 .stream()
@@ -242,6 +275,15 @@ private String generateAccessUrlForOpenAccessS3Object(AwsS3AccessObject awsS3Acc
             awsS3AccessObject.getKey();
     }
 
+    private String generateAccessUrlForManifestObject(String id) {
+        return drsConfig.scheme() +
+            "://" +
+            drsConfig.hostDomain() +
+            "/ga4gh/drs/v1/objects/" +
+            id +
+            "/manifest-content";
+    }
+
     private SingleDrsObjectAuthInfoResponseDTO generateAuthInfoForSingleDrsObjectId(String id) {
         return new SingleDrsObjectAuthInfoResponseDTO(
             id,
diff --git a/src/main/java/org/ga4gh/refcloud/api/security/GA4GHPassportTokenEvaluator.java b/src/main/java/org/ga4gh/refcloud/api/security/GA4GHPassportTokenEvaluator.java
index 3f3486cb..c58eb051 100644
--- a/src/main/java/org/ga4gh/refcloud/api/security/GA4GHPassportTokenEvaluator.java
+++ b/src/main/java/org/ga4gh/refcloud/api/security/GA4GHPassportTokenEvaluator.java
@@ -1,6 +1,7 @@
 package org.ga4gh.refcloud.api.security;
 
 import org.springframework.stereotype.Component;
+import org.ga4gh.refcloud.api.core.dataset.DatasetService;
 import org.ga4gh.refcloud.api.drs.authinfo.MultiDrsObjectAuthInfoRequestDTO;
 import org.ga4gh.refcloud.api.drs.authinfo.MultiDrsObjectRequestDTO;
 import org.ga4gh.refcloud.api.drs.authinfo.SingleDrsObjectRequestDTO;
@@ -19,13 +20,24 @@ public class GA4GHPassportTokenEvaluator {
 
     private final DrsObjectService drsObjectService;
 
-    public GA4GHPassportTokenEvaluator(JwtDecoder jwtDecoder, DrsObjectService drsObjectService) {
+    private final DatasetService datasetService;
+
+    public GA4GHPassportTokenEvaluator(JwtDecoder jwtDecoder, DrsObjectService drsObjectService, DatasetService datasetService) {
         this.jwtDecoder = jwtDecoder;
         this.drsObjectService = drsObjectService;
+        this.datasetService = datasetService;
+    }
+
+    public boolean canAccessDataset(Authentication authentication, String datasetId) {
+        if (authentication == null || !(authentication.getPrincipal() instanceof Jwt jwt)) {
+            return false;
+        }
+
+        String userId = jwt.getSubject();
+        return datasetService.validateUserIsAuthorizedForDataset(userId, datasetId);
     }
 
     public boolean canAccessDrsObject(Authentication authentication, String objectId) {
-        // Sanity check the authentication context
         if (authentication == null || !(authentication.getPrincipal() instanceof Jwt jwt)) {
             return false;
         }
diff --git a/src/main/java/org/ga4gh/refcloud/api/security/SecurityConfig.java b/src/main/java/org/ga4gh/refcloud/api/security/SecurityConfig.java
index 2ece8e98..143704ae 100644
--- a/src/main/java/org/ga4gh/refcloud/api/security/SecurityConfig.java
+++ b/src/main/java/org/ga4gh/refcloud/api/security/SecurityConfig.java
@@ -23,14 +23,20 @@ public class SecurityConfig {
 
     private final OrySessionFilter orySessionFilter;
 
+    private static final List<RequestMatcher> ORY_KRATOS_SESSION_ENDPOINTS = List.of(
+        PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.GET, "/datasets"),
+        PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.GET, "/datasets/{datasetId}"),
+        PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.POST, "/datasets/{datasetId}/request-access")
+    );
+
     private static final List<RequestMatcher> PUBLIC_ENDPOINTS = List.of(
-        // DRS API
         PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.OPTIONS, "/ga4gh/drs/v1/objects/{id}"),
         PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.GET, "/ga4gh/drs/v1/service-info")
     );
 
     private static final List<RequestMatcher> CUSTOM_SECURITY_ENDPOINTS = List.of(
-        // DRS API
+        PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.GET, "/datasets/{datasetId}/manifests"),
+        PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.GET, "/ga4gh/drs/v1/objects/{id}"),
         PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.POST, "/ga4gh/drs/v1/objects/{id}"),
         PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.OPTIONS, "/ga4gh/drs/v1/objects"),
         PathPatternRequestMatcher.withDefaults().matcher(HttpMethod.POST, "/ga4gh/drs/v1/objects")
@@ -61,7 +67,7 @@ public SecurityFilterChain oryKratosSessionFilterChain(HttpSecurity http) throws
             // Disable standard CSRF/sessions since we are an API validated by Ory Kratos tokens
             .csrf(csrf -> csrf.disable())
             .sessionManagement(session -> session.sessionCreationPolicy(SessionCreationPolicy.STATELESS))
-            .securityMatcher("/datasets/**")
+            .securityMatcher(new OrRequestMatcher(ORY_KRATOS_SESSION_ENDPOINTS))
             .authorizeHttpRequests(auth -> auth
                 .anyRequest().authenticated() // endpoints that require kratos session token
             )
@@ -92,6 +98,7 @@ public SecurityFilterChain customSecurityEndpointsFilterChain(HttpSecurity http)
             .authorizeHttpRequests(authorize -> authorize
                 .anyRequest().permitAll()
             )
+            .oauth2ResourceServer(oauth2 -> oauth2.jwt(jwt -> {}))
             .csrf(csrf -> csrf.disable())
             .sessionManagement(session -> session.disable());
 
diff --git a/src/main/java/org/ga4gh/refcloud/api/utils/HibernateJackson3BridgeConfig.java b/src/main/java/org/ga4gh/refcloud/api/utils/HibernateJackson3BridgeConfig.java
new file mode 100644
index 00000000..ad64efb3
--- /dev/null
+++ b/src/main/java/org/ga4gh/refcloud/api/utils/HibernateJackson3BridgeConfig.java
@@ -0,0 +1,37 @@
+package org.ga4gh.refcloud.api.utils;
+
+import org.hibernate.cfg.AvailableSettings;
+import org.hibernate.type.descriptor.java.JavaType;
+import org.hibernate.type.format.FormatMapper;
+import org.hibernate.type.descriptor.WrapperOptions;
+import org.springframework.boot.hibernate.autoconfigure.HibernatePropertiesCustomizer;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+
+// Make sure your ObjectMapper import matches your active Jackson 3 package
+// Typically: import tools.jackson.databind.ObjectMapper;
+import tools.jackson.databind.ObjectMapper; 
+
+@Configuration
+public class HibernateJackson3BridgeConfig {
+
+    @Bean
+    public HibernatePropertiesCustomizer jsonFormatMapperCustomizer(ObjectMapper objectMapper) {
+        return hibernateProperties -> 
+            hibernateProperties.put(AvailableSettings.JSON_FORMAT_MAPPER, new FormatMapper() {
+                
+                @Override
+                public <T> T fromString(CharSequence charSequence, JavaType<T> javaType, WrapperOptions wrapperOptions) {
+                    // Bridge Hibernate's JavaType to Jackson 3's TypeFactory layout
+                    var jacksonType = objectMapper.getTypeFactory().constructType(javaType.getJavaType());
+                    return objectMapper.readValue(charSequence.toString(), jacksonType);
+                }
+
+                @Override
+                public <T> String toString(T value, JavaType<T> javaType, WrapperOptions wrapperOptions) {
+                    // Serialize the object safely to string using Jackson 3
+                    return objectMapper.writeValueAsString(value);
+                }
+            });
+    }
+}
\ No newline at end of file
diff --git a/src/main/resources/application.yml b/src/main/resources/application.yml
index 45a0f0bf..04c9bfa4 100644
--- a/src/main/resources/application.yml
+++ b/src/main/resources/application.yml
@@ -43,7 +43,8 @@ ga4gh:
           username: kratos_webhook_user
           password: secret
     drs:
-      host-domain: localhost:8080
+      scheme: http
+      host-domain: 127.0.0.1:8080
       service-info:
         id: org.ga4gh.refcloud.drs.local
         name: GA4GH Reference Cloud DRS Service (Local Dev Environment)
diff --git a/src/test/resources/sql/add-test-data.sql b/src/test/resources/sql/add-test-data.sql
index 99ae9aaf..8cc62a4d 100644
--- a/src/test/resources/sql/add-test-data.sql
+++ b/src/test/resources/sql/add-test-data.sql
@@ -80,16 +80,57 @@ INSERT INTO passport_visa (id, name, description, dataset_id) VALUES
 
 
 INSERT INTO drs_object (id, description, created_time, mime_type, name, size, updated_time, version, dataset_id) VALUES
-    ('drs.id.0', '1000 Genomes Phase3 WGS alignment BAM: HG00096 chr11', '2015-05-13 03:10:08', 'application/x-bam', 'HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam', 692760649, '2015-05-13 03:10:08', 'v1', 'ds1');
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam', 'HG00096 whole-exome bam file', '2015-05-13 03:30:44', 'application/octet-stream', 'HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam', 9196950908, '2015-05-13 03:30:44', 'v1', 'ds1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai', 'HG00096 whole-exome bai file', '2015-05-13 03:12:41', 'application/octet-stream', 'HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai', 6842584, '2015-05-13 03:12:41', 'v1', 'ds1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas', 'HG00096 whole-exome bas file', '2015-05-13 03:29:43', 'application/octet-stream', 'HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas', 827, '2015-05-13 03:29:43', 'v1', 'ds1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram', 'HG00096 whole-exome cram file', '2015-05-13 03:13:58', 'application/octet-stream', 'HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram', 2304099249, '2015-05-13 03:13:58', 'v1', 'ds1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai', 'HG00096 whole-exome crai file', '2015-05-13 03:27:40', 'application/octet-stream', 'HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai', 178859, '2015-05-13 03:27:40', 'v1', 'ds1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra', 'HG00096 whole-exome csra file', '2015-05-13 03:14:58', 'application/octet-stream', 'HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra', 2282395745, '2015-05-13 03:14:58', 'v1', 'ds1');
 
 INSERT INTO drs_object_alias (drs_object_id, alias) VALUES
-    ('drs.id.0', 'HG00096 chr11 BAM'),
-    ('drs.id.0', 'HG00096 chr11 BAM file');
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam', 'HG00096 whole-exome bam file'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai', 'HG00096 whole-exome bai file'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas', 'HG00096 whole-exome bas file'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram', 'HG00096 whole-exome cram file'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai', 'HG00096 whole-exome crai file'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra', 'HG00096 whole-exome csra file');
 
 INSERT INTO drs_object_checksum(drs_object_id, checksum, type) VALUES
-    ('drs.id.0', 'e2425c6f57b2aa4ddb08f472d98221d0', 'md5'),
-    ('drs.id.0', '9dddead4e1b13471784e536824ffed3c6137126a', 'sha1'),
-    ('drs.id.0', '718f74b48fd739c9305bbf6c3d4b29ef3c9d62fcb1c16eaae61dbfd0c5db60d5', 'sha256');
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam', '5d4ae7a46d470036d99429c363498965', 'md5'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam', '72d9fc6f08feb87b5e9666eb6bee98bd00b0d024', 'sha1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam', 'e2062842263d1ca42ce4368e61850b75a58f34cd9b6347c465ea95e3da31d943', 'sha256'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai', 'a8a1f1ba420f7d75c7955b04b5972c54', 'md5'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai', '56e7a1d55713e74eccf220365bbeec69ced899ad', 'sha1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai', '89d6677f9e8d54fd3d771177ab352fb5d7435cf4ad1fb5dec33e5a508612f5c0', 'sha256'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas', 'e2ebae06af6ce9c92750339e9a85e5d9', 'md5'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas', 'a3327258093db7eea317b41dff596a032e7e27cf', 'sha1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas', 'fb028f0d383e9cc8e987c287a263191c9f910963dc4ad0c68094d569ba714033', 'sha256'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram', '46d0f8f93809c608571d82c327bb8bfc', 'md5'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram', 'bbc73bcee7a1e837d5541db1857611b75288a53f', 'sha1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram', '5b8da495309e4b1a2fa229557a2f4ccb7be9347b75fac6c37bc845cb0dcf0784', 'sha256'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai', '83ef6855b01965759b9c3c9c7e6586a8', 'md5'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai', 'b7d52204789cc5e098a6be807083165a8a34f4f6', 'sha1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai', '722260f9c8757ed603cfb1bf7441e076371028c05e3f89a81930c895254837ee', 'sha256'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra', '35e12569cd5dacb4d158832bedfb8b1b', 'md5'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra', '8f1f9634ab8118717471420a5703fb10ee5383b6', 'sha1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra', 'd5b7a372c4c0187590b3a73b4fd79a4913ad1900305694cb2a33051e63684e89', 'sha256');
 
 INSERT INTO aws_s3_access_object(drs_object_id, region, bucket, key) VALUES
-    ('drs.id.0', 'us-east-1', '1000genomes', '/phase3/data/HG00096/alignment/HG00096.chrom11.ILLUMINA.bwa.GBR.low_coverage.20120522.bam');
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam', 'us-east-1', '1000genomes', '/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai', 'us-east-1', '1000genomes', '/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas', 'us-east-1', '1000genomes', '/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram', 'us-east-1', '1000genomes', '/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai', 'us-east-1', '1000genomes', '/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra', 'us-east-1', '1000genomes', '/phase3/data/HG00096/exome_alignment/HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra');
+
+/* DRS Object Manifest */
+INSERT INTO drs_object (id, description, created_time, mime_type, name, size, updated_time, version, dataset_id, is_manifest, manifest_content) VALUES
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.MANIFEST', 'HG00096 whole-exome - compound object manifest', '2015-05-13 03:30:44', 'application/json', 'HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.MANIFEST', 416, '2015-05-13 03:30:44', 'v1', 'ds1', true, '{"bam_file":"HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam","bai_file":"HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bai","bas_file":"HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.bas","cram_file":"HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram","crai_file":"HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.cram.crai","csra_file":"HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.bam.csra"}');
+
+INSERT INTO drs_object_alias (drs_object_id, alias) VALUES
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.MANIFEST', 'HG00096 whole-exome - compound object manifest');
+
+INSERT INTO drs_object_checksum(drs_object_id, checksum, type) VALUES
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.MANIFEST', 'f257d781e1d4017d1a851b61acc7e93c', 'md5'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.MANIFEST', 'f9db5b1a3332972dbe499399543f210b88dbe55c', 'sha1'),
+    ('HG00096.mapped.ILLUMINA.bwa.GBR.exome.20120522.MANIFEST', 'e5a3e248d68a035d23e2ed336c93aaf78cd46aceca7cd814e58689896f97b33c', 'sha256');
\ No newline at end of file