Additional changes. Went to Hibernate 6, encountered issues with the

version of java.  Backed down to 5 but ran into different issues

HIRS_AttestationCA/src/main/java/hirs/attestationca/AbstractAttestationCertificateAuthority.java

@@ -30,7 +30,6 @@ import hirs.data.persist.info.TPMInfo;
 import hirs.data.service.DeviceRegister;
 import hirs.persist.CertificateManager;
 import hirs.persist.DeviceManager;
-import hirs.persist.ReferenceDigestManager;
 import hirs.persist.ReferenceEventManager;
 import hirs.persist.ReferenceManifestManager;
 import hirs.persist.TPM2ProvisionerState;
@@ -179,7 +178,6 @@ public abstract class AbstractAttestationCertificateAuthority
     private final ReferenceManifestManager referenceManifestManager;
     private final DeviceRegister deviceRegister;
     private final DeviceManager deviceManager;
-    private final ReferenceDigestManager referenceDigestManager;
     private final ReferenceEventManager referenceEventManager;
     private String tpmQuoteHash = "";
     private String tpmQuoteSignature = "";
@@ -195,7 +193,6 @@ public abstract class AbstractAttestationCertificateAuthority
      * @param deviceRegister the device register
      * @param validDays the number of days issued certs are valid
      * @param deviceManager the device manager
-     * @param referenceDigestManager the reference digest manager
      * @param referenceEventManager the reference event manager
      */
     @SuppressWarnings("checkstyle:parameternumber")
@@ -207,7 +204,6 @@ public abstract class AbstractAttestationCertificateAuthority
             final ReferenceManifestManager referenceManifestManager,
             final DeviceRegister deviceRegister, final int validDays,
             final DeviceManager deviceManager,
-            final ReferenceDigestManager referenceDigestManager,
             final ReferenceEventManager referenceEventManager) {
         this.supplyChainValidationService = supplyChainValidationService;
         this.privateKey = privateKey;
@@ -218,7 +214,6 @@ public abstract class AbstractAttestationCertificateAuthority
         this.deviceRegister = deviceRegister;
         this.validDays = validDays;
         this.deviceManager = deviceManager;
-        this.referenceDigestManager = referenceDigestManager;
         this.referenceEventManager = referenceEventManager;
     }
 

HIRS_AttestationCA/src/main/java/hirs/attestationca/rest/RestfulAttestationCertificateAuthority.java

@@ -5,7 +5,6 @@ import hirs.attestationca.service.SupplyChainValidationService;
 import hirs.data.service.DeviceRegister;
 import hirs.persist.CertificateManager;
 import hirs.persist.DeviceManager;
-import hirs.persist.ReferenceDigestManager;
 import hirs.persist.ReferenceEventManager;
 import hirs.persist.ReferenceManifestManager;
 import hirs.structs.converters.StructConverter;
@@ -41,7 +40,6 @@ public class RestfulAttestationCertificateAuthority
      * @param deviceRegister the device register
      * @param validDays the number of days issued certs are valid
      * @param deviceManager the device manager
-     * @param referenceDigestManager the reference digest manager
      * @param referenceEventManager the reference event manager
      */
     @SuppressWarnings({ "checkstyle:parameternumber" })
@@ -54,13 +52,12 @@ public class RestfulAttestationCertificateAuthority
             final ReferenceManifestManager referenceManifestManager,
             final DeviceRegister deviceRegister,
             final DeviceManager deviceManager,
-            final ReferenceDigestManager referenceDigestManager,
             final ReferenceEventManager referenceEventManager,
             @Value("${aca.certificates.validity}") final int validDays) {
         super(supplyChainValidationService, privateKey, acaCertificate, structConverter,
                 certificateManager, referenceManifestManager,
                 deviceRegister, validDays, deviceManager,
-                referenceDigestManager, referenceEventManager);
+                referenceEventManager);
     }
 
     /*

HIRS_AttestationCA/src/test/java/hirs/attestationca/AbstractAttestationCertificateAuthorityTest.java

@@ -132,7 +132,7 @@ public class AbstractAttestationCertificateAuthorityTest {
     public void setup() {
         aca = new AbstractAttestationCertificateAuthority(null, keyPair.getPrivate(),
                 null, null, null, null, null, 1,
-                null, null, null) {
+                null, null) {
         };
     }
 

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/CommonPageConfiguration.java

@@ -7,6 +7,8 @@ import org.springframework.context.annotation.ComponentScan;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
+import org.springframework.stereotype.Repository;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
 import org.springframework.web.multipart.commons.CommonsMultipartResolver;
 import org.springframework.web.servlet.ViewResolver;
 import org.springframework.web.servlet.config.annotation.EnableWebMvc;
@@ -19,7 +21,9 @@ import java.nio.charset.StandardCharsets;
  * Specifies the location to scan for page controllers, view resolver for JSON data, and view
  * resolver to map view names to jsp files.
  */
+@Repository
 @Configuration
+@EnableTransactionManagement
 @EnableWebMvc
 @ComponentScan("hirs.attestationca.portal.page.controllers")
 @Import({ PersistenceConfiguration.class })

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/CertificateDetailsPageController.java

@@ -8,9 +8,9 @@ import hirs.persist.CertificateManager;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.io.IOException;
@@ -22,8 +22,8 @@ import static hirs.attestationca.portal.page.Page.CERTIFICATE_DETAILS;
 /**
  * Controller for the Certificate Details page.
  */
-@Controller
+@RestController
-@RequestMapping("/certificate-details")
+@RequestMapping(path = "/certificate-details")
 public class CertificateDetailsPageController extends PageController<CertificateDetailsPageParams> {
 
     /**
@@ -31,6 +31,7 @@ public class CertificateDetailsPageController extends PageController<Certificate
      */
     static final String INITIAL_DATA = "initialData";
 
+    @Autowired
     private final CertificateManager certificateManager;
     private static final Logger LOGGER =
             LogManager.getLogger(CertificateDetailsPageController.class);

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/CertificateRequestPageController.java

@@ -26,14 +26,15 @@ import org.hibernate.criterion.Restrictions;
 import org.hibernate.sql.JoinType;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.util.StreamUtils;
+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.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.multipart.MultipartFile;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
@@ -57,11 +58,13 @@ import static org.apache.logging.log4j.LogManager.getLogger;
 /**
  * Controller for the Certificates list all pages.
  */
-@Controller
+@RestController
-@RequestMapping("/certificate-request")
+@RequestMapping(path = "/certificate-request")
 public class CertificateRequestPageController extends PageController<NoPageParams> {
 
+    @Autowired
     private final CertificateManager certificateManager;
+    @Autowired
     private final OrderedListQuerier<Certificate> dataTableQuerier;
 
     private CertificateAuthorityCredential certificateAuthorityCredential;
@@ -127,6 +130,7 @@ public class CertificateRequestPageController extends PageController<NoPageParam
      * redirect.
      * @return the path for the view and data model for the page.
      */
+    @GetMapping
     @RequestMapping("/{certificateType}")
     public ModelAndView initPage(@PathVariable("certificateType") final String certificateType,
             final NoPageParams params, final Model model) {
@@ -168,6 +172,7 @@ public class CertificateRequestPageController extends PageController<NoPageParam
      * @return the data table
      */
     @ResponseBody
+    @GetMapping
     @RequestMapping(value = "/{certificateType}/list",
             produces = MediaType.APPLICATION_JSON_VALUE,
             method = RequestMethod.GET)

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/DevicesPageController.java

@@ -1,19 +1,26 @@
 package hirs.attestationca.portal.page.controllers;
 
+import hirs.FilteredRecordsList;
 import hirs.attestationca.portal.datatables.DataTableInput;
 import hirs.attestationca.portal.datatables.DataTableResponse;
 import hirs.attestationca.portal.datatables.OrderedListQueryDataTableAdapter;
-import static hirs.attestationca.portal.page.Page.DEVICES;
 import hirs.attestationca.portal.page.PageController;
 import hirs.attestationca.portal.page.params.NoPageParams;
+import hirs.data.persist.Device;
+import hirs.data.persist.certificate.Certificate;
+import hirs.data.persist.certificate.DeviceAssociatedCertificate;
+import hirs.persist.DBManager;
+import hirs.persist.DeviceManager;
 import org.apache.logging.log4j.Logger;
+import org.hibernate.criterion.Restrictions;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.util.ArrayList;
@@ -22,23 +29,19 @@ import java.util.HashMap;
 import java.util.List;
 import java.util.UUID;
 
+import static hirs.attestationca.portal.page.Page.DEVICES;
 import static org.apache.logging.log4j.LogManager.getLogger;
-import org.hibernate.criterion.Restrictions;
-import hirs.FilteredRecordsList;
-import hirs.data.persist.Device;
-import hirs.data.persist.certificate.Certificate;
-import hirs.data.persist.certificate.DeviceAssociatedCertificate;
-import hirs.persist.DBManager;
-import hirs.persist.DeviceManager;
 
 /**
  * Controller for the Device page.
  */
-@Controller
+@RestController
-@RequestMapping("/devices")
+@RequestMapping(path = "/devices")
 public class DevicesPageController extends PageController<NoPageParams> {
 
+    @Autowired
     private final DeviceManager deviceManager;
+    @Autowired
     private final DBManager<Certificate> certificateDBManager;
     private static final Logger LOGGER = getLogger(DevicesPageController.class);
 
@@ -76,6 +79,7 @@ public class DevicesPageController extends PageController<NoPageParams> {
      * @return the data tables response, including the result set and paging information
      */
     @ResponseBody
+    @GetMapping
     @RequestMapping(value = "list", produces = MediaType.APPLICATION_JSON_VALUE,
             method = RequestMethod.GET)
     public DataTableResponse<HashMap<String, Object>> getTableData(

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/HelpController.java

@@ -1,24 +1,26 @@
 package hirs.attestationca.portal.page.controllers;
 
-import static hirs.attestationca.portal.page.Page.HELP;
 import hirs.attestationca.portal.page.PageController;
 import hirs.attestationca.portal.page.params.NoPageParams;
-import java.io.File;
-import java.io.IOException;
-import static org.apache.logging.log4j.LogManager.getLogger;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.context.ApplicationContext;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.servlet.ModelAndView;
 
+import java.io.File;
+import java.io.IOException;
+
+import static hirs.attestationca.portal.page.Page.HELP;
+import static org.apache.logging.log4j.LogManager.getLogger;
+
 /**
  * Controller for the Help page.
  */
-@Controller
+@RestController
-@RequestMapping("/help")
+@RequestMapping(path = "/help")
 public class HelpController extends PageController<NoPageParams> {
 
     @Autowired

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/PolicyPageController.java

@@ -12,11 +12,12 @@ import hirs.persist.PolicyManager;
 import hirs.persist.PolicyManagerException;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.ModelAttribute;
 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.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
 import org.springframework.web.servlet.view.RedirectView;
@@ -31,8 +32,8 @@ import static org.apache.logging.log4j.LogManager.getLogger;
 /**
  * Controller for the Policy page.
  */
-@Controller
+@RestController
-@RequestMapping("/policy")
+@RequestMapping(path = "/policy")
 public class PolicyPageController extends PageController<NoPageParams> {
 
     private static final Logger LOGGER = getLogger(PolicyPageController.class);
@@ -45,7 +46,9 @@ public class PolicyPageController extends PageController<NoPageParams> {
 
     private static final String ENABLED_EXPIRES_PARAMETER_VALUE = "expires";
 
+    @Autowired
     private PolicyManager policyManager;
+    @Autowired
     private AppraiserManager appraiserManager;
 
     /**
@@ -108,6 +111,7 @@ public class PolicyPageController extends PageController<NoPageParams> {
      * @return View containing the url and parameters
      * @throws URISyntaxException if malformed URI
      */
+    @GetMapping
     @RequestMapping(value = "update-pc-validation", method = RequestMethod.POST)
     public RedirectView updatePcVal(@ModelAttribute final PolicyPageModel ppModel,
             final RedirectAttributes attr) throws URISyntaxException {
@@ -159,6 +163,7 @@ public class PolicyPageController extends PageController<NoPageParams> {
      * @return View containing the url and parameters
      * @throws URISyntaxException if malformed URI
      */
+    @GetMapping
     @RequestMapping(value = "update-pc-attribute-validation", method = RequestMethod.POST)
     public RedirectView updatePcAttributeVal(@ModelAttribute final PolicyPageModel ppModel,
             final RedirectAttributes attr)

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/ReferenceManifestDetailsPageController.java

@@ -25,9 +25,9 @@ import hirs.validation.SupplyChainValidatorException;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.io.IOException;
@@ -47,14 +47,18 @@ import java.util.UUID;
 /**
  * Controller for the Reference Manifest Details page.
  */
-@Controller
+@RestController
-@RequestMapping("/rim-details")
+@RequestMapping(path = "/rim-details")
 public class ReferenceManifestDetailsPageController
         extends PageController<ReferenceManifestDetailsPageParams> {
 
+    @Autowired
     private final ReferenceManifestManager referenceManifestManager;
+    @Autowired
     private final ReferenceDigestManager referenceDigestManager;
+    @Autowired
     private final ReferenceEventManager referenceEventManager;
+    @Autowired
     private final CertificateManager certificateManager;
     private static final ReferenceManifestValidator RIM_VALIDATOR
             = new ReferenceManifestValidator();

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/ReferenceManifestPageController.java

@@ -30,13 +30,14 @@ import org.hibernate.Criteria;
 import org.hibernate.criterion.Restrictions;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
 import org.springframework.util.StreamUtils;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.RequestParam;
 import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.multipart.MultipartFile;
 import org.springframework.web.servlet.ModelAndView;
 import org.springframework.web.servlet.mvc.support.RedirectAttributes;
@@ -66,8 +67,8 @@ import java.util.zip.ZipOutputStream;
 /**
  * Controller for the Reference Manifest page.
  */
-@Controller
+@RestController
-@RequestMapping("/reference-manifests")
+@RequestMapping(path = "/reference-manifests")
 public class ReferenceManifestPageController
         extends PageController<NoPageParams> {
 
@@ -75,7 +76,9 @@ public class ReferenceManifestPageController
     private static final String LOG_FILE_PATTERN = "([^\\s]+(\\.(?i)(rimpcr|rimel|bin|log))$)";
 
     private final BiosDateValidator biosValidator;
+    @Autowired
     private final ReferenceManifestManager referenceManifestManager;
+    @Autowired
     private final ReferenceEventManager referenceEventManager;
     private static final Logger LOGGER
             = LogManager.getLogger(ReferenceManifestPageController.class);
@@ -161,6 +164,7 @@ public class ReferenceManifestPageController
      * information
      */
     @ResponseBody
+    @GetMapping
     @RequestMapping(value = "/list",
             produces = MediaType.APPLICATION_JSON_VALUE,
             method = RequestMethod.GET)

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/RimDatabasePageController.java

@@ -23,11 +23,12 @@ import org.hibernate.Criteria;
 import org.hibernate.criterion.Restrictions;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.servlet.ModelAndView;
 
 import java.text.DateFormat;
@@ -37,8 +38,8 @@ import java.text.SimpleDateFormat;
 /**
  * Controller for the TPM Events page.
  */
-@Controller
+@RestController
-@RequestMapping("/rim-database")
+@RequestMapping(path = "/rim-database")
 public class RimDatabasePageController
         extends PageController<NoPageParams> {
 
@@ -131,6 +132,7 @@ public class RimDatabasePageController
      * information
      */
     @ResponseBody
+    @GetMapping
     @RequestMapping(value = "/list",
             produces = MediaType.APPLICATION_JSON_VALUE,
             method = RequestMethod.GET)

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/page/controllers/ValidationReportsPageController.java

@@ -22,11 +22,12 @@ import org.hibernate.Criteria;
 import org.hibernate.criterion.Restrictions;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.http.MediaType;
-import org.springframework.stereotype.Controller;
 import org.springframework.ui.Model;
+import org.springframework.web.bind.annotation.GetMapping;
 import org.springframework.web.bind.annotation.RequestMapping;
 import org.springframework.web.bind.annotation.RequestMethod;
 import org.springframework.web.bind.annotation.ResponseBody;
+import org.springframework.web.bind.annotation.RestController;
 import org.springframework.web.servlet.ModelAndView;
 
 import javax.servlet.http.HttpServletRequest;
@@ -52,12 +53,15 @@ import static org.apache.logging.log4j.LogManager.getLogger;
 /**
  * Controller for the Validation Reports page.
  */
-@Controller
+@RestController
-@RequestMapping("/validation-reports")
+@RequestMapping(path = "/validation-reports")
 public class ValidationReportsPageController extends PageController<NoPageParams> {
 
+    @Autowired
     private final CrudManager<SupplyChainValidationSummary> supplyChainValidatorSummaryManager;
+    @Autowired
     private final CertificateManager certificateManager;
+    @Autowired
     private final DeviceManager deviceManager;
 
     private static String systemColumnHeaders = "Verified Manufacturer,"
@@ -105,6 +109,7 @@ public class ValidationReportsPageController extends PageController<NoPageParams
      * @return the data table response containing the supply chain summary records
      */
     @ResponseBody
+    @GetMapping
     @RequestMapping(value = "list", produces = MediaType.APPLICATION_JSON_VALUE,
             method = RequestMethod.GET)
     public DataTableResponse<SupplyChainValidationSummary> getTableData(

HIRS_AttestationCAPortal/src/main/java/hirs/attestationca/portal/persistence/PersistenceConfiguration.java

@@ -20,11 +20,15 @@ import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.Import;
 import org.springframework.orm.hibernate5.LocalSessionFactoryBean;
+import org.springframework.stereotype.Repository;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 /**
  * Spring configuration class for persistence beans used by the Attestation CA Portal.
  */
+@Repository
 @Configuration
+@EnableTransactionManagement
 @Import({ HibernateConfiguration.class })
 public class PersistenceConfiguration {
 

HIRS_Utils/build.gradle

@@ -33,7 +33,6 @@ dependencies {
     compile libs.commons_http
     compile libs.commons_valid
     compile libs.hibernate
-//    compile libs.hikari
     compile libs.jackson
     compile libs.jadira_usertype
     compile libs.joda_time

HIRS_Utils/src/main/java/hirs/data/persist/AbstractEntity.java

@@ -1,8 +1,5 @@
 package hirs.data.persist;
 
-import org.hibernate.annotations.GenericGenerator;
-import org.hibernate.annotations.Type;
-
 import javax.persistence.Column;
 import javax.persistence.GeneratedValue;
 import javax.persistence.Id;
@@ -25,8 +22,6 @@ public abstract class AbstractEntity {
     @Id
     @Column(name = "id")
     @GeneratedValue(generator = "uuid2")
-    @GenericGenerator(name = "uuid2", strategy = "uuid2")
-    @Type(type = "uuid-char")
     private UUID id;
 
     @Column (name = "create_time")

HIRS_Utils/src/main/java/hirs/data/persist/ReferenceManifest.java

@@ -5,7 +5,6 @@ import com.google.common.base.Preconditions;
 import org.apache.commons.codec.binary.Hex;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.hibernate.annotations.Type;
 
 import javax.persistence.Access;
 import javax.persistence.AccessType;
@@ -91,7 +90,6 @@ public abstract class ReferenceManifest extends ArchivableEntity {
     private String platformModel = null;
     @Column(nullable = false)
     private String fileName = null;
-    @Type(type = "uuid-char")
     @Column
     private UUID associatedRim;
     @Column

HIRS_Utils/src/main/java/hirs/data/persist/State.java

@@ -1,7 +1,8 @@
 package hirs.data.persist;
 
-import java.util.Date;
+import org.apache.logging.log4j.LogManager;
-import java.util.UUID;
+import org.apache.logging.log4j.Logger;
+
 import javax.persistence.Access;
 import javax.persistence.AccessType;
 import javax.persistence.Column;
@@ -10,9 +11,8 @@ import javax.persistence.Id;
 import javax.persistence.Inheritance;
 import javax.persistence.InheritanceType;
 import javax.persistence.Table;
-import org.apache.logging.log4j.LogManager;
+import java.util.Date;
-import org.apache.logging.log4j.Logger;
+import java.util.UUID;
-import org.hibernate.annotations.Type;
 
 /**
  * The <code>State</code> class represents a state. This is an abstract class
@@ -33,7 +33,6 @@ public abstract class State {
 
     @Id
     @Column(name = "id")
-    @Type(type = "uuid-char")
     private final UUID id;
 
     @Column (nullable = false)

HIRS_Utils/src/main/java/hirs/data/persist/info/NetworkInfo.java

@@ -2,18 +2,16 @@ package hirs.data.persist.info;
 
 import hirs.data.persist.DeviceInfoReport;
 import hirs.data.persist.InetAddressXmlAdapter;
-import java.io.Serializable;
+import org.apache.logging.log4j.LogManager;
-import java.net.InetAddress;
+import org.apache.logging.log4j.Logger;
-import java.util.Arrays;
 
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
-
+import java.io.Serializable;
-import org.apache.logging.log4j.Logger;
+import java.net.InetAddress;
-import org.apache.logging.log4j.LogManager;
+import java.util.Arrays;
-import org.hibernate.annotations.Type;
 
 /**
  * This class is used to represent the network info of a device.
@@ -33,7 +31,7 @@ public class NetworkInfo implements Serializable {
     @XmlElement
     @XmlJavaTypeAdapter(value = InetAddressXmlAdapter.class)
     @Column(length = DeviceInfoReport.SHORT_STRING_LENGTH, nullable = true)
-    @Type(type = "hirs.data.persist.type.InetAddressType")
+    //@Type(type = "hirs.data.persist.type.InetAddressType")
     private InetAddress ipAddress;
 
     @XmlElement

HIRS_Utils/src/main/java/hirs/data/persist/info/TPMInfo.java

@@ -3,20 +3,17 @@ package hirs.data.persist.info;
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import hirs.data.persist.DeviceInfoReport;
 import hirs.data.persist.X509CertificateAdapter;
-
+import hirs.utils.StringValidator;
-import java.io.Serializable;
+import org.apache.logging.log4j.LogManager;
-import java.security.cert.X509Certificate;
+import org.apache.logging.log4j.Logger;
 
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
 import javax.persistence.Lob;
 import javax.xml.bind.annotation.XmlElement;
 import javax.xml.bind.annotation.adapters.XmlJavaTypeAdapter;
-
+import java.io.Serializable;
-import hirs.utils.StringValidator;
+import java.security.cert.X509Certificate;
-import org.apache.logging.log4j.Logger;
-import org.apache.logging.log4j.LogManager;
-import org.hibernate.annotations.Type;
 
 /**
  * This class is used to represent the TPM information for a device.
@@ -49,7 +46,7 @@ public class TPMInfo implements Serializable {
     @XmlElement
     @XmlJavaTypeAdapter(X509CertificateAdapter.class)
     @Lob
-    @Type(type = "hirs.data.persist.type.X509CertificateType")
+//    @Type(type = "hirs.data.persist.type.X509CertificateType")
     @JsonIgnore
     private X509Certificate identityCertificate;
 

HIRS_Utils/src/main/java/hirs/persist/AbstractDbManager.java

@@ -16,6 +16,7 @@ import org.hibernate.criterion.MatchMode;
 import org.hibernate.criterion.Restrictions;
 import org.hibernate.query.Query;
 import org.hibernate.service.spi.ServiceRegistryImplementor;
+import org.springframework.stereotype.Service;
 
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -38,6 +39,7 @@ import static org.hibernate.criterion.Restrictions.sqlRestriction;
  *
  * @param <T> type of objects to manage by this manager
  */
+@Service
 public abstract class AbstractDbManager<T> implements CrudManager<T> {
 
     private static final Logger LOGGER = LogManager.getLogger(AbstractDbManager.class);

HIRS_Utils/src/main/java/hirs/persist/DBAppraiserManager.java

@@ -4,6 +4,7 @@ import hirs.appraiser.Appraiser;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.hibernate.SessionFactory;
+import org.springframework.stereotype.Service;
 
 import java.util.List;
 
@@ -11,6 +12,7 @@ import java.util.List;
  * This class defines a <code>ApprasierManager</code> that stores the
  * appraisers in a database.
  */
+@Service
 public class DBAppraiserManager extends DBManager<Appraiser> implements AppraiserManager {
     private static final Logger LOGGER = LogManager.getLogger();
 

HIRS_Utils/src/main/java/hirs/persist/DBCertificateManager.java

@@ -7,6 +7,7 @@ import org.hibernate.SessionFactory;
 import org.springframework.retry.RetryCallback;
 import org.springframework.retry.RetryContext;
 import org.springframework.retry.support.RetryTemplate;
+import org.springframework.stereotype.Service;
 
 import java.io.Serializable;
 import java.util.HashSet;
@@ -15,6 +16,7 @@ import java.util.Set;
 /**
  * This class is used to persist and retrieve {@link Certificate}s into and from a database.
  */
+@Service
 public class DBCertificateManager extends DBManager<Certificate>
         implements CertificateManager {
 

HIRS_Utils/src/main/java/hirs/persist/DBDeviceGroupManager.java

@@ -10,6 +10,7 @@ import org.hibernate.Session;
 import org.hibernate.SessionFactory;
 import org.hibernate.Transaction;
 import org.hibernate.query.Query;
+import org.springframework.stereotype.Service;
 
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -25,6 +26,7 @@ import java.util.Set;
  * This class defines the <code>DBDeviceGroupManager</code> that is used to
  * store <code>DeviceGroup</code>s in the database.
  */
+@Service
 public class DBDeviceGroupManager extends DBManager<DeviceGroup> implements DeviceGroupManager {
 
     private static final Logger LOGGER = LogManager.getLogger(DBDeviceGroupManager.class);

HIRS_Utils/src/main/java/hirs/persist/DBDeviceManager.java

@@ -11,6 +11,7 @@ import org.hibernate.Session;
 import org.hibernate.SessionFactory;
 import org.hibernate.Transaction;
 import org.hibernate.query.Query;
+import org.springframework.stereotype.Service;
 
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -29,6 +30,7 @@ import java.util.Set;
  * This class defines a <code>DeviceManager</code> that stores the devices
  * in a database.
  */
+@Service
 public class DBDeviceManager extends DBManager<Device> implements
         DeviceManager {
 

HIRS_Utils/src/main/java/hirs/persist/DBManager.java

@@ -15,6 +15,7 @@ import org.springframework.retry.RetryListener;
 import org.springframework.retry.backoff.FixedBackOffPolicy;
 import org.springframework.retry.policy.SimpleRetryPolicy;
 import org.springframework.retry.support.RetryTemplate;
+import org.springframework.stereotype.Service;
 
 import javax.persistence.criteria.Predicate;
 import java.io.Serializable;
@@ -29,6 +30,7 @@ import java.util.Map;
  * archive, and delete operations for managing objects in a database.
  *
  */
+@Service
 public class DBManager<T> extends AbstractDbManager<T> {
     private static final Logger LOGGER = LogManager.getLogger(DBManager.class);
 

HIRS_Utils/src/main/java/hirs/persist/DBPolicyManager.java

@@ -11,6 +11,7 @@ import org.hibernate.Session;
 import org.hibernate.SessionFactory;
 import org.hibernate.Transaction;
 import org.hibernate.query.Query;
+import org.springframework.stereotype.Repository;
 
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -23,6 +24,7 @@ import java.util.List;
  * This class defines a <code>PolicyManager</code> that stores policies in a
  * database.
  */
+@Repository
 public class DBPolicyManager extends DBManager<Policy> implements PolicyManager {
 
     private static final Logger LOGGER = LogManager.getLogger(DBPolicyManager.class);

HIRS_Utils/src/main/java/hirs/persist/DBPortalInfoManager.java

@@ -1,19 +1,20 @@
 package hirs.persist;
 
-import hirs.data.persist.info.PortalInfo;
 import hirs.data.persist.enums.PortalScheme;
-
+import hirs.data.persist.info.PortalInfo;
-import java.net.URI;
-import java.net.URISyntaxException;
-
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.hibernate.SessionFactory;
+import org.springframework.stereotype.Service;
+
+import java.net.URI;
+import java.net.URISyntaxException;
 
 /**
  * A <code>DBPortalInfoManager</code> is a service (extends <code>DBManager</code>) that
  * implements the <code>PortalInfoManager</code> that stores and retrieves Portal Info objects.
  */
+@Service
 public class DBPortalInfoManager extends DBManager<PortalInfo> implements PortalInfoManager {
 
     private static final Logger LOGGER = LogManager.getLogger(DBPortalInfoManager.class);

HIRS_Utils/src/main/java/hirs/persist/DBReferenceEventManager.java

@@ -11,6 +11,7 @@ import org.hibernate.Session;
 import org.hibernate.SessionFactory;
 import org.hibernate.Transaction;
 import org.hibernate.query.Query;
+import org.springframework.stereotype.Service;
 
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -26,6 +27,7 @@ import java.util.UUID;
  * This class is used to persist and retrieve {@link hirs.data.persist.ReferenceDigestValue}s into
  * and from the database.
  */
+@Service
 public class DBReferenceEventManager  extends DBManager<ReferenceDigestValue>
         implements ReferenceEventManager {
 

HIRS_Utils/src/main/java/hirs/persist/DBReferenceManifestManager.java

@@ -3,7 +3,7 @@ package hirs.persist;
 import hirs.data.persist.ReferenceManifest;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
-import org.hibernate.SessionFactory;
+import org.springframework.stereotype.Service;
 import org.xml.sax.SAXException;
 
 import javax.persistence.criteria.CriteriaBuilder;
@@ -20,6 +20,7 @@ import java.util.Set;
  * This class is used to persist and retrieve {@link ReferenceManifest}s into
  * and from the database.
  */
+@Service
 public class DBReferenceManifestManager extends DBManager<ReferenceManifest>
         implements ReferenceManifestManager {
 

HIRS_Utils/src/main/java/hirs/persist/DBReportManager.java

@@ -8,6 +8,7 @@ import org.hibernate.criterion.Conjunction;
 import org.hibernate.criterion.Disjunction;
 import org.hibernate.criterion.MatchMode;
 import org.hibernate.criterion.Restrictions;
+import org.springframework.stereotype.Service;
 
 import java.util.List;
 import java.util.Map;
@@ -20,6 +21,7 @@ import static org.hibernate.criterion.Restrictions.ilike;
  * This class defines a <code>ReportManager</code> that stores the reports in a
  * database.
  */
+@Service
 public class DBReportManager extends DBManager<Report> implements ReportManager {
     private static final Logger LOGGER = getLogger(DBReportManager.class);
 

HIRS_Utils/src/main/java/hirs/persist/DBReportRequestStateManager.java

@@ -5,6 +5,7 @@ import hirs.data.persist.ReportRequestState;
 import org.apache.logging.log4j.LogManager;
 import org.apache.logging.log4j.Logger;
 import org.hibernate.SessionFactory;
+import org.springframework.stereotype.Service;
 
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.Predicate;
@@ -17,6 +18,7 @@ import java.util.List;
  * This class defines a <code>ReportRequestStateManager</code> that stores ReportRequestStates in a
  * database.
  */
+@Service
 public class DBReportRequestStateManager extends DBManager<ReportRequestState>
         implements ReportRequestStateManager {
     private static final Logger LOGGER = LogManager.getLogger(DBReportRequestStateManager.class);

HIRS_Utils/src/main/java/hirs/persist/DBReportSummaryManager.java

@@ -7,6 +7,7 @@ import org.hibernate.SessionFactory;
 import org.hibernate.Transaction;
 import org.hibernate.criterion.Order;
 import org.hibernate.query.Query;
+import org.springframework.stereotype.Service;
 
 import javax.persistence.criteria.CriteriaBuilder;
 import javax.persistence.criteria.CriteriaQuery;
@@ -23,6 +24,7 @@ import static org.apache.logging.log4j.LogManager.getLogger;
  * report
  * summary in a database.
  */
+@Service
 public class DBReportSummaryManager extends DBManager<ReportSummary>
         implements ReportSummaryManager {
 

HIRS_Utils/src/main/java/hirs/persist/DBRepositoryManager.java

@@ -3,6 +3,7 @@ package hirs.persist;
 import hirs.repository.RepoPackage;
 import hirs.repository.Repository;
 import org.hibernate.SessionFactory;
+import org.springframework.stereotype.Service;
 
 import java.io.Serializable;
 import java.util.List;
@@ -11,6 +12,7 @@ import java.util.List;
  * This class defines a {@link RepositoryManager} that stores Repositories and RepoPackages
  * in a database.
  */
+@Service
 public class DBRepositoryManager implements RepositoryManager {
     private final DBManager<Repository> repositoryDBManager;
     private final DBManager<RepoPackage> repoPackageDBManager;

HIRS_Utils/src/main/java/hirs/persist/DeviceManager.java

@@ -2,6 +2,7 @@ package hirs.persist;
 
 import hirs.FilteredRecordsList;
 import hirs.data.persist.Device;
+import org.springframework.stereotype.Repository;
 
 import java.util.List;
 import java.util.Set;
@@ -11,6 +12,7 @@ import java.util.Set;
  * <code>DeviceManager</code> is used to store and manage devices. It has
  * support for the basic create, read, update, and delete methods.
  */
+@Repository
 public interface DeviceManager extends OrderedListQuerier<Device> {
 
     /**

HIRS_Utils/src/main/java/hirs/persist/HibernateConfiguration.java

@@ -1,18 +1,19 @@
 package hirs.persist;
 
-import com.zaxxer.hikari.HikariDataSource;
-import org.hibernate.SessionFactory;
 import org.springframework.beans.factory.annotation.Value;
 import org.springframework.context.annotation.Bean;
 import org.springframework.context.annotation.Configuration;
 import org.springframework.context.annotation.PropertySource;
 import org.springframework.context.annotation.PropertySources;
 import org.springframework.context.support.PropertySourcesPlaceholderConfigurer;
+import org.springframework.jdbc.datasource.DriverManagerDataSource;
 import org.springframework.orm.hibernate5.HibernateTransactionManager;
 import org.springframework.orm.hibernate5.LocalSessionFactoryBean;
 import org.springframework.transaction.annotation.EnableTransactionManagement;
 
 import javax.sql.DataSource;
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Properties;
 
 /**
@@ -86,14 +87,16 @@ public class HibernateConfiguration {
      */
     @Bean
     public DataSource dataSource() {
-        HikariDataSource dataSource = new HikariDataSource();
+        DriverManagerDataSource dataSource = new DriverManagerDataSource();
-        dataSource.setJdbcUrl(url);
+        dataSource.setUrl(url);
         dataSource.setUsername(username);
         dataSource.setPassword(password);
         dataSource.setDriverClassName(driverClass);
-        dataSource.setMaximumPoolSize(Integer.parseInt(maximumPoolSize));
+
-        dataSource.setConnectionTimeout(Long.parseLong(connectionTimeout));
+//        dataSource.setMaximumPoolSize(Integer.parseInt(maximumPoolSize));
-        dataSource.setLeakDetectionThreshold(Long.parseLong(leakDetectionThreshold));
+//        dataSource.setConnectionTimeout(Long.parseLong(connectionTimeout));
+//        dataSource.setLeakDetectionThreshold(Long.parseLong(leakDetectionThreshold));
+
         return dataSource;
     }
 
@@ -121,26 +124,71 @@ public class HibernateConfiguration {
      */
     @Bean
     public LocalSessionFactoryBean sessionFactory() {
-        LocalSessionFactoryBean sessionFactory = new LocalSessionFactoryBean();
+        // Hibernate 5.4 SessionFactory example without XML
-        sessionFactory.setDataSource(dataSource());
+        Map<String, String> settings = new HashMap<>();
+        settings.put("connection.driver_class", "com.mysql.jdbc.Driver");
+        settings.put("dialect", "org.hibernate.dialect.MySQL8Dialect");
+        settings.put("hibernate.connection.url",
+                "jdbc:mysql://localhost/hibernate_examples");
+        settings.put("hibernate.connection.username", "root");
+        settings.put("hibernate.connection.password", "root");
+        settings.put("hibernate.current_session_context_class", "thread");
+        settings.put("hibernate.show_sql", "true");
+        settings.put("hibernate.format_sql", "true");
+
+        ServiceRegistry serviceRegistry = new StandardServiceRegistryBuilder()
+                .applySettings(settings).build();
+
+        MetadataSources metadataSources = new MetadataSources(serviceRegistry);
+        // metadataSources.addAnnotatedClass(Player.class);
+        Metadata metadata = metadataSources.buildMetadata();
+
+        // here we build the SessionFactory (Hibernate 5.4)
+        LocalSessionFactoryBean sessionFactory = (LocalSessionFactoryBean) metadata
+                .getSessionFactoryBuilder()
+                .build();
         sessionFactory.setHibernateProperties(hibernateProperties());
         sessionFactory.setPackagesToScan("hirs");
         return sessionFactory;
     }
 
+//    public static SessionFactory getCurrentSessionFromJPA() {
+//        // JPA and Hibernate SessionFactory example
+//        EntityManagerFactory emf =
+//                Persistence.createEntityManagerFactory("jpa-tutorial");
+//        EntityManager entityManager = emf.createEntityManager();
+//        // Get the Hibernate Session from the EntityManager in JPA
+//        Session session = entityManager.unwrap(org.hibernate.Session.class);
+//        SessionFactory factory = session.getSessionFactory();
+//        return factory;
+//    }
+
+//    /**
+//     * Configures a session factory bean that in turn configures the hibernate session factory.
+//     * Enables auto scanning of annotations such that entities do not need to be registered in a
+//     * hibernate configuration file.
+//     *
+//     * @return session factory
+//     */
+//    @Bean
+//    public LocalSessionFactoryBean sessionFactory() {
+//        LocalSessionFactoryBean sessionFactory = new LocalSessionFactoryBean();
+//        sessionFactory.setDataSource(dataSource());
+//        sessionFactory.setHibernateProperties(hibernateProperties());
+//        sessionFactory.setPackagesToScan("hirs");
+//        return sessionFactory;
+//    }
+
     /**
      * Configure a transaction manager for the hibernate session factory.
      *
      * @return transaction manager
      */
     @Bean
-    public HibernateTransactionManager transactionManager() {
+    public HibernateTransactionManager getTransactionManager() {
-        SessionFactory sessionFactory = sessionFactory().getObject();
+        HibernateTransactionManager transactionManager = new HibernateTransactionManager();
-        if (sessionFactory != null) {
+        transactionManager.setSessionFactory(sessionFactory().getObject());
-            return new HibernateTransactionManager(sessionFactory);
+        return transactionManager;
-        } else {
-            return new HibernateTransactionManager();
-        }
     }
 
     /**

HIRS_Utils/src/main/java/hirs/persist/ScheduledJobInfo.java

@@ -1,6 +1,5 @@
 package hirs.persist;
 
-import org.hibernate.annotations.Type;
 import org.joda.time.Interval;
 import org.joda.time.LocalDateTime;
 import org.joda.time.LocalTime;
@@ -8,7 +7,6 @@ import org.joda.time.Period;
 
 import javax.persistence.Column;
 import javax.persistence.Embeddable;
-
 import java.util.Date;
 
 /**
@@ -26,7 +24,6 @@ public class ScheduledJobInfo {
     public static final LocalTime DEFAULT_START_TIME = new LocalTime(22, 0, 0);
 
     @Column
-    @Type(type = "org.jadira.usertype.dateandtime.joda.PersistentLocalTime")
     private LocalTime startTime;
 
     @Column

HIRS_Utils/src/main/java/hirs/repository/RepoPackage.java

@@ -2,7 +2,6 @@ package hirs.repository;
 
 import com.fasterxml.jackson.annotation.JsonIgnore;
 import hirs.data.persist.Digest;
-import org.hibernate.annotations.Type;
 
 import javax.persistence.CascadeType;
 import javax.persistence.Column;
@@ -33,7 +32,6 @@ import java.util.UUID;
 public abstract class RepoPackage {
     @Id
     @Column(name = "id")
-    @Type(type = "uuid-char")
     private UUID id;
 
     @Column

HIRS_Utils/src/main/java/hirs/utils/MySqlUtf8CompatibleDialect.java

@@ -1,6 +1,6 @@
 package hirs.utils;
 
-import org.hibernate.dialect.MySQL5InnoDBDialect;
+import org.hibernate.dialect.MySQLDialect;
 
 /**
  * This class is a shim on top of the standard MySQL5InnoDBDialect to set the row format
@@ -24,7 +24,7 @@ import org.hibernate.dialect.MySQL5InnoDBDialect;
  * https://dev.mysql.com/doc/refman/5.7/en/innodb-row-format-dynamic.html
  * https://dev.mysql.com/doc/refman/5.5/en/innodb-restrictions.html
  */
-public class MySqlUtf8CompatibleDialect extends MySQL5InnoDBDialect {
+public class MySqlUtf8CompatibleDialect extends MySQLDialect {
     /**
      * Returns the table 'type' string, which specifies the storage engine (via the
      * super call) and appends the desired row format.

build.gradle

@@ -106,10 +106,9 @@ subprojects {
       findbugs:      'com.google.code.findbugs:findbugs:3.0.0',
       gson:          'com.google.code.gson:gson:2.9.0',
       guava:         'com.google.guava:guava:31.1-jre',
-      hibernate:   [ 'org.hibernate.common:hibernate-commons-annotations:5.0.0.Final',
+      hibernate:   [ 'org.hibernate.common:hibernate-commons-annotations:5.1.1.Final',
-                     'org.hibernate:hibernate-core:5.0.0.Final',
+                     'org.hibernate:hibernate-core:5.2.4.Final',
-                     'org.hibernate:hibernate-hikaricp:5.0.0.Final'],
+                     'org.hibernate:hibernate-hikaricp:5.2.4.Final'],
-//      hikari:        'com.zaxxer:HikariCP:5.0.1',
       hsqldb:        'org.hsqldb:hsqldb:2.6.1',
       http:          'org.apache.httpcomponents:httpclient:4.5.13',
       jackson:      [ 'com.fasterxml.jackson.core:jackson-core:2.13.2',