From 0966fa407bca1b6aef964dfd6f865c95a0ccd8e2 Mon Sep 17 00:00:00 2001
From: Rick Herrick <jrherrick@wustl.edu>
Date: Thu, 28 Apr 2016 17:47:11 -0500
Subject: [PATCH] Now having functioning site managed with preferences classes.
---
.../java/org/nrg/dcm/DicomSCPManager.java | 61 +-
.../org/nrg/schedule/TriggerTaskProxy.java | 36 -
src/main/java/org/nrg/user/daos/UserDAO.java | 33 -
src/main/java/org/nrg/user/entities/User.java | 44 -
.../org/nrg/user/services/UserService.java | 18 -
.../impl/hibernate/HibernateUserService.java | 31 -
.../nrg/xapi/rest/event/EventHandlerApi.java | 24 +-
.../xnat/configuration/ApplicationConfig.java | 106 +++
.../xnat/configuration/ConfigResolver.java | 41 -
.../xnat/configuration/FeaturesConfig.java | 12 +-
.../org/nrg/xnat/configuration/MqConfig.java | 9 +
.../configuration/NotificationsConfig.java | 2 +-
.../org/nrg/xnat/configuration/OrmConfig.java | 120 +++
.../xnat/configuration/PrearchiveConfig.java | 15 -
.../xnat/configuration/PreferencesConfig.java | 2 +-
.../nrg/xnat/configuration/ReactorConfig.java | 35 +-
.../xnat/configuration/SchedulerConfig.java | 43 +-
.../configuration/SiteConfigPreferences.java | 881 ------------------
.../AutomationEventScriptHandler.java | 524 ++++++-----
.../DatabaseConfig.java | 69 +-
.../InitializerSiteConfiguration.java | 154 ---
.../xnat/initialization/InitializingTask.java | 15 +
.../InitializingTasksExecutor.java | 38 +
.../PropertiesConfig.java | 2 +-
.../nrg/xnat/initialization/RootConfig.java | 112 +--
.../initialization/XnatWebAppInitializer.java | 22 +-
.../tasks/AbstractInitializingTask.java | 35 +
.../tasks/EncryptXnatPasswords.java | 86 ++
.../tasks/GetSiteWideAnonScript.java | 48 +
.../tasks/GetSiteWidePETTracerList.java | 53 ++
.../tasks/UpdateNewSecureDefinitions.java | 36 +
.../tasks/UpdateUserAuthTable.java | 62 ++
.../restlet/services/SettingsRestlet.java | 17 +-
.../restlet/servlet/XNATRestletServlet.java | 94 --
...rSecurityInterceptorBeanPostProcessor.java | 23 +-
.../nrg/xnat/security/ResetFailedLogins.java | 24 +-
.../security/XnatExpiredPasswordFilter.java | 71 +-
.../security/XnatLdapUserDetailsMapper.java | 29 +-
.../xnat/security/XnatPasswordEncrypter.java | 71 --
.../xnat/security/XnatProviderManager.java | 68 +-
.../AliasTokenAuthenticationProvider.java | 8 +-
.../alias/ClearExpiredAliasTokens.java | 12 +-
...aseAuthenticationProviderConfigurator.java | 18 +-
...dapAuthenticationProviderConfigurator.java | 14 +-
.../XnatDatabaseAuthenticationProvider.java | 18 +-
.../XnatDatabaseUserDetailsService.java | 35 +-
.../org/nrg/xnat/utils/XnatUserProvider.java | 6 +-
.../xnat/entities/xnat-entity-packages.txt | 12 +
.../WEB-INF/conf/TurbineResources.properties | 6 +-
src/main/webapp/WEB-INF/conf/mq-context.xml | 11 +-
.../webapp/WEB-INF/conf/xnat-conf.properties | 6 +-
51 files changed, 1244 insertions(+), 2068 deletions(-)
delete mode 100644 src/main/java/org/nrg/schedule/TriggerTaskProxy.java
delete mode 100644 src/main/java/org/nrg/user/daos/UserDAO.java
delete mode 100644 src/main/java/org/nrg/user/entities/User.java
delete mode 100644 src/main/java/org/nrg/user/services/UserService.java
delete mode 100644 src/main/java/org/nrg/user/services/impl/hibernate/HibernateUserService.java
create mode 100644 src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
delete mode 100644 src/main/java/org/nrg/xnat/configuration/ConfigResolver.java
create mode 100644 src/main/java/org/nrg/xnat/configuration/MqConfig.java
create mode 100644 src/main/java/org/nrg/xnat/configuration/OrmConfig.java
delete mode 100644 src/main/java/org/nrg/xnat/configuration/PrearchiveConfig.java
delete mode 100644 src/main/java/org/nrg/xnat/configuration/SiteConfigPreferences.java
rename src/main/java/org/nrg/xnat/{configuration => initialization}/DatabaseConfig.java (60%)
delete mode 100644 src/main/java/org/nrg/xnat/initialization/InitializerSiteConfiguration.java
create mode 100644 src/main/java/org/nrg/xnat/initialization/InitializingTask.java
create mode 100644 src/main/java/org/nrg/xnat/initialization/InitializingTasksExecutor.java
rename src/main/java/org/nrg/xnat/{configuration => initialization}/PropertiesConfig.java (99%)
create mode 100644 src/main/java/org/nrg/xnat/initialization/tasks/AbstractInitializingTask.java
create mode 100644 src/main/java/org/nrg/xnat/initialization/tasks/EncryptXnatPasswords.java
create mode 100644 src/main/java/org/nrg/xnat/initialization/tasks/GetSiteWideAnonScript.java
create mode 100644 src/main/java/org/nrg/xnat/initialization/tasks/GetSiteWidePETTracerList.java
create mode 100644 src/main/java/org/nrg/xnat/initialization/tasks/UpdateNewSecureDefinitions.java
create mode 100644 src/main/java/org/nrg/xnat/initialization/tasks/UpdateUserAuthTable.java
delete mode 100644 src/main/java/org/nrg/xnat/security/XnatPasswordEncrypter.java
create mode 100644 src/main/resources/META-INF/xnat/entities/xnat-entity-packages.txt
diff --git a/src/main/java/org/nrg/dcm/DicomSCPManager.java b/src/main/java/org/nrg/dcm/DicomSCPManager.java
index dc51a81a..8b7b3e3f 100644
--- a/src/main/java/org/nrg/dcm/DicomSCPManager.java
+++ b/src/main/java/org/nrg/dcm/DicomSCPManager.java
@@ -10,17 +10,18 @@
*/
package org.nrg.dcm;
-import org.nrg.config.services.SiteConfigurationService;
import org.nrg.dcm.preferences.DicomSCPInstance;
import org.nrg.dcm.preferences.DicomSCPPreference;
import org.nrg.framework.exceptions.NrgServiceError;
import org.nrg.framework.exceptions.NrgServiceException;
import org.nrg.framework.exceptions.NrgServiceRuntimeException;
+import org.nrg.xdat.preferences.SiteConfigPreferences;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
import javax.annotation.PreDestroy;
-import javax.inject.Inject;
import java.io.IOException;
import java.util.ArrayList;
import java.util.HashMap;
@@ -37,44 +38,44 @@ public class DicomSCPManager {
public DicomSCP create(final DicomSCPInstance instance) throws NrgServiceException {
final String scpId = instance.getScpId();
- if (_preferences.hasDicomSCPInstance(scpId)) {
+ if (_dicomScpPreferences.hasDicomSCPInstance(scpId)) {
throw new NrgServiceException(NrgServiceError.ConfigurationError, "There is already a DICOM SCP instance with the ID " + scpId);
}
try {
- _preferences.setDicomSCPInstance(instance);
- return _preferences.getDicomSCP(scpId);
+ _dicomScpPreferences.setDicomSCPInstance(instance);
+ return _dicomScpPreferences.getDicomSCP(scpId);
} catch (IOException e) {
throw new NrgServiceRuntimeException(NrgServiceError.Unknown, "Unable to create DICOM SCP: " + instance.getAeTitle() + ":" + instance.getPort(), e);
}
}
public void delete(final String scpId) throws NrgServiceException {
- if (!_preferences.hasDicomSCPInstance(scpId)) {
+ if (!_dicomScpPreferences.hasDicomSCPInstance(scpId)) {
throw new NrgServiceException(NrgServiceError.UnknownEntity, "There is no DICOM SCP instance with the ID " + scpId);
}
- _preferences.deleteDicomSCPInstance(scpId);
+ _dicomScpPreferences.deleteDicomSCPInstance(scpId);
}
public List<DicomSCPInstance> getDicomSCPInstances() {
- return new ArrayList<>(_preferences.getDicomSCPInstances().values());
+ return new ArrayList<>(_dicomScpPreferences.getDicomSCPInstances().values());
}
public void setDicomSCPInstance(final DicomSCPInstance instance) {
try {
- _preferences.setDicomSCPInstance(instance);
+ _dicomScpPreferences.setDicomSCPInstance(instance);
} catch (IOException e) {
throw new NrgServiceRuntimeException(NrgServiceError.Unknown, "Unable to update DICOM SCP: " + instance.getAeTitle() + ":" + instance.getPort(), e);
}
}
public List<String> startOrStopDicomSCPAsDictatedByConfiguration() {
- final boolean enableDicomReceiver = _siteConfigurationService.getBoolSiteConfigurationProperty("enableDicomReceiver", true);
+ final boolean enableDicomReceiver = _siteConfigPreferences.isEnableDicomReceiver();
return enableDicomReceiver ? startDicomSCPs() : stopDicomSCPs();
}
public List<String> startDicomSCPs() {
final List<String> started = new ArrayList<>();
- for (final DicomSCPInstance instance : _preferences.getDicomSCPInstances().values()) {
+ for (final DicomSCPInstance instance : _dicomScpPreferences.getDicomSCPInstances().values()) {
if (instance.isEnabled()) {
startDicomSCP(instance);
started.add(instance.getScpId());
@@ -84,12 +85,12 @@ public class DicomSCPManager {
}
public void startDicomSCP(final String scpId) {
- startDicomSCP(_preferences.getDicomSCPInstance(scpId));
+ startDicomSCP(_dicomScpPreferences.getDicomSCPInstance(scpId));
}
public List<String> stopDicomSCPs() {
final List<String> stopped = new ArrayList<>();
- for (final DicomSCP dicomSCP : _preferences.getDicomSCPs()) {
+ for (final DicomSCP dicomSCP : _dicomScpPreferences.getDicomSCPs()) {
if (dicomSCP.isStarted()) {
dicomSCP.stop();
stopped.add(dicomSCP.getScpId());
@@ -99,12 +100,12 @@ public class DicomSCPManager {
}
public void stopDicomSCP(final String scpId) {
- final DicomSCPInstance instance = _preferences.getDicomSCPInstance(scpId);
+ final DicomSCPInstance instance = _dicomScpPreferences.getDicomSCPInstance(scpId);
if (instance == null) {
throw new NrgServiceRuntimeException(NrgServiceError.UnknownEntity, "Couldn't find the DICOM SCP instance identified by " + scpId);
}
try {
- final DicomSCP dicomSCP = _preferences.getDicomSCP(scpId);
+ final DicomSCP dicomSCP = _dicomScpPreferences.getDicomSCP(scpId);
if (dicomSCP != null) {
if (dicomSCP.isStarted()) {
dicomSCP.stop();
@@ -116,13 +117,13 @@ public class DicomSCPManager {
}
public void enableDicomSCP(final String scpId) {
- final DicomSCPInstance instance = _preferences.getDicomSCPInstance(scpId);
+ final DicomSCPInstance instance = _dicomScpPreferences.getDicomSCPInstance(scpId);
try {
if (!instance.isEnabled()) {
instance.setEnabled(true);
- _preferences.setDicomSCPInstance(instance);
+ _dicomScpPreferences.setDicomSCPInstance(instance);
}
- final DicomSCP dicomSCP = _preferences.getDicomSCP(scpId);
+ final DicomSCP dicomSCP = _dicomScpPreferences.getDicomSCP(scpId);
if (!dicomSCP.isStarted()) {
dicomSCP.start();
}
@@ -132,13 +133,13 @@ public class DicomSCPManager {
}
public void disableDicomSCP(final String scpId) {
- final DicomSCPInstance instance = _preferences.getDicomSCPInstance(scpId);
+ final DicomSCPInstance instance = _dicomScpPreferences.getDicomSCPInstance(scpId);
try {
if (instance.isEnabled()) {
instance.setEnabled(false);
- _preferences.setDicomSCPInstance(instance);
+ _dicomScpPreferences.setDicomSCPInstance(instance);
}
- final DicomSCP dicomSCP = _preferences.getDicomSCP(scpId);
+ final DicomSCP dicomSCP = _dicomScpPreferences.getDicomSCP(scpId);
if (dicomSCP.isStarted()) {
dicomSCP.stop();
}
@@ -149,23 +150,23 @@ public class DicomSCPManager {
public Map<String, Boolean> areDicomSCPsStarted() {
final Map<String, Boolean> statuses = new HashMap<>();
- for (final DicomSCP dicomSCP : _preferences.getDicomSCPs()) {
+ for (final DicomSCP dicomSCP : _dicomScpPreferences.getDicomSCPs()) {
statuses.put(dicomSCP.getScpId(), dicomSCP.isStarted());
}
return statuses;
}
public boolean hasDicomSCP(final String scpId) {
- return _preferences.hasDicomSCPInstance(scpId);
+ return _dicomScpPreferences.hasDicomSCPInstance(scpId);
}
public DicomSCPInstance getDicomSCPInstance(final String scpId) {
- return _preferences.getDicomSCPInstance(scpId);
+ return _dicomScpPreferences.getDicomSCPInstance(scpId);
}
private void startDicomSCP(final DicomSCPInstance instance) {
try {
- final DicomSCP dicomSCP = _preferences.getDicomSCP(instance.getScpId());
+ final DicomSCP dicomSCP = _dicomScpPreferences.getDicomSCP(instance.getScpId());
dicomSCP.start();
} catch (IOException e) {
throw new NrgServiceRuntimeException(NrgServiceError.Unknown, "Unable to start DICOM SCP: " + instance.getAeTitle() + ":" + instance.getPort(), e);
@@ -174,9 +175,11 @@ public class DicomSCPManager {
private static final Logger _log = LoggerFactory.getLogger(DicomSCPManager.class);
- @Inject
- private SiteConfigurationService _siteConfigurationService;
+ @Autowired
+ @Lazy
+ private DicomSCPPreference _dicomScpPreferences;
- @Inject
- private DicomSCPPreference _preferences;
+ @Autowired
+ @Lazy
+ private SiteConfigPreferences _siteConfigPreferences;
}
diff --git a/src/main/java/org/nrg/schedule/TriggerTaskProxy.java b/src/main/java/org/nrg/schedule/TriggerTaskProxy.java
deleted file mode 100644
index 562b88d5..00000000
--- a/src/main/java/org/nrg/schedule/TriggerTaskProxy.java
+++ /dev/null
@@ -1,36 +0,0 @@
-package org.nrg.schedule;
-
-import org.springframework.scheduling.Trigger;
-import org.springframework.scheduling.config.TriggerTask;
-import org.springframework.scheduling.support.CronTrigger;
-import org.springframework.scheduling.support.PeriodicTrigger;
-
-import java.util.concurrent.TimeUnit;
-
-public class TriggerTaskProxy extends TriggerTask {
- public TriggerTaskProxy(final Runnable runnable, final long period) {
- this(runnable, period, null);
- }
-
- public TriggerTaskProxy(final Runnable runnable, final long period, final TimeUnit timeUnit) {
- this(runnable, new PeriodicTrigger(period, timeUnit));
- }
-
- public TriggerTaskProxy(final Runnable runnable, final long period, final int initialDelay) {
- this(runnable, period, null, initialDelay);
- }
-
- public TriggerTaskProxy(final Runnable runnable, final long period, final TimeUnit timeUnit, final int initialDelay) {
- this(runnable, new PeriodicTrigger(period, timeUnit) {{
- setInitialDelay(initialDelay);
- }});
- }
-
- public TriggerTaskProxy(final Runnable runnable, final String expression) {
- this(runnable, new CronTrigger(expression));
- }
-
- public TriggerTaskProxy(final Runnable runnable, final Trigger trigger) {
- super(runnable, trigger);
- }
-}
diff --git a/src/main/java/org/nrg/user/daos/UserDAO.java b/src/main/java/org/nrg/user/daos/UserDAO.java
deleted file mode 100644
index c8dd55c9..00000000
--- a/src/main/java/org/nrg/user/daos/UserDAO.java
+++ /dev/null
@@ -1,33 +0,0 @@
-/*
- * org.nrg.user.daos.UserDAO
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.user.daos;
-
-import org.hibernate.Criteria;
-import org.hibernate.criterion.Restrictions;
-import org.nrg.framework.orm.hibernate.AbstractHibernateDAO;
-import org.nrg.user.entities.User;
-import org.springframework.stereotype.Repository;
-
-@Repository
-public class UserDAO extends AbstractHibernateDAO<User> {
-
- /**
- * @param name
- * @return
- */
- public User getUserByName(String name) {
- Criteria criteria = getSession().createCriteria(getParameterizedType());
- criteria.add(Restrictions.eq("name", name));
- criteria.add(Restrictions.eq("enabled", true));
- return (User) criteria.list().get(0);
- }
-
-}
diff --git a/src/main/java/org/nrg/user/entities/User.java b/src/main/java/org/nrg/user/entities/User.java
deleted file mode 100644
index 78ebb5fa..00000000
--- a/src/main/java/org/nrg/user/entities/User.java
+++ /dev/null
@@ -1,44 +0,0 @@
-/*
- * org.nrg.user.entities.User
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 9/5/13 2:38 PM
- */
-package org.nrg.user.entities;
-
-import org.hibernate.annotations.Cache;
-import org.hibernate.annotations.CacheConcurrencyStrategy;
-import org.nrg.framework.orm.hibernate.AbstractHibernateEntity;
-import org.nrg.framework.orm.hibernate.annotations.Auditable;
-
-import javax.persistence.Entity;
-import javax.persistence.Table;
-import javax.persistence.UniqueConstraint;
-
-@Auditable
-@Entity
-@Table(uniqueConstraints = @UniqueConstraint(columnNames = {"name"}))
-@Cache(usage = CacheConcurrencyStrategy.READ_WRITE, region = "nrg")
-public class User extends AbstractHibernateEntity {
- private static final long serialVersionUID = -163628363303918602L;
-
- /**
- * @param name Sets the name property.
- */
- public void setName(String name) {
- _name = name;
- }
-
- /**
- * @return Returns the name property.
- */
- public String getName() {
- return _name;
- }
-
- private String _name;
-}
diff --git a/src/main/java/org/nrg/user/services/UserService.java b/src/main/java/org/nrg/user/services/UserService.java
deleted file mode 100644
index b2051d95..00000000
--- a/src/main/java/org/nrg/user/services/UserService.java
+++ /dev/null
@@ -1,18 +0,0 @@
-/*
- * org.nrg.user.services.UserService
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.user.services;
-
-import org.nrg.framework.orm.hibernate.BaseHibernateService;
-import org.nrg.user.entities.User;
-
-public interface UserService extends BaseHibernateService<User> {
- abstract public User getUserByName(String name);
-}
diff --git a/src/main/java/org/nrg/user/services/impl/hibernate/HibernateUserService.java b/src/main/java/org/nrg/user/services/impl/hibernate/HibernateUserService.java
deleted file mode 100644
index 897a08f7..00000000
--- a/src/main/java/org/nrg/user/services/impl/hibernate/HibernateUserService.java
+++ /dev/null
@@ -1,31 +0,0 @@
-/*
- * org.nrg.user.services.impl.hibernate.HibernateUserService
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.user.services.impl.hibernate;
-
-import org.nrg.framework.orm.hibernate.AbstractHibernateEntityService;
-import org.nrg.user.daos.UserDAO;
-import org.nrg.user.entities.User;
-import org.nrg.user.services.UserService;
-import org.springframework.stereotype.Service;
-import org.springframework.transaction.annotation.Transactional;
-
-@Service
-public class HibernateUserService extends AbstractHibernateEntityService<User, UserDAO> implements UserService {
-
- /**
- * @see org.nrg.user.services.UserService#getUserByName(java.lang.String)
- */
- @Override
- @Transactional
- public User getUserByName(String name) {
- return getDao().getUserByName(name);
- }
-}
diff --git a/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java b/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java
index fc39acce..1e0ad096 100644
--- a/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java
+++ b/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java
@@ -20,6 +20,7 @@ import org.nrg.xft.security.UserI;
import org.nrg.xnat.event.conf.EventPackages;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.core.annotation.AnnotationUtils;
import org.springframework.http.HttpStatus;
import org.springframework.http.ResponseEntity;
@@ -49,13 +50,16 @@ public class EventHandlerApi {
private static final Logger _log = LoggerFactory.getLogger(EventHandlerApi.class);
/** The event ids service. */
+ @Autowired
private HibernateAutomationEventIdsService eventIdsService;
/** The filters service. */
+ @Autowired
private HibernateAutomationFiltersService filtersService;
/** The event packages. */
- private static EventPackages eventPackages;
+ @Autowired
+ private EventPackages eventPackages;
/**
* Inits the this.
@@ -64,7 +68,6 @@ public class EventHandlerApi {
private void initThis() {
getEventIdsService();
getFiltersService();
- getEventPackages();
}
/**
@@ -82,7 +85,7 @@ public class EventHandlerApi {
if (status != null) {
return new ResponseEntity<>(status);
}
- return new ResponseEntity<List<EventClassInfo>>(getEventInfoList(project_id), HttpStatus.OK);
+ return new ResponseEntity<>(getEventInfoList(project_id), HttpStatus.OK);
}
/**
@@ -99,7 +102,7 @@ public class EventHandlerApi {
if (status != null) {
return new ResponseEntity<>(status);
}
- return new ResponseEntity<List<EventClassInfo>>(getEventInfoList(null), HttpStatus.OK);
+ return new ResponseEntity<>(getEventInfoList(null), HttpStatus.OK);
}
/**
@@ -190,7 +193,6 @@ public class EventHandlerApi {
private List<String> getEventClassList(List<AutomationEventIds> eventIdsList) {
final List<String> classList = Lists.newArrayList();
// ClassList should be pulled from available event classes rather than from events
- final EventPackages eventPackages = getEventPackages();
if (eventPackages != null) {
for (final String pkg : eventPackages) {
try {
@@ -243,18 +245,6 @@ public class EventHandlerApi {
return filtersService;
}
- /**
- * Gets the event packages.
- *
- * @return the event packages
- */
- private static EventPackages getEventPackages() {
- if (eventPackages == null) {
- eventPackages = XDAT.getContextService().getBean("eventPackages",EventPackages.class);
- }
- return eventPackages;
- }
-
/**
* Gets the session user.
*
diff --git a/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java b/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
new file mode 100644
index 00000000..0a2d8fd0
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
@@ -0,0 +1,106 @@
+package org.nrg.xnat.configuration;
+
+import org.nrg.config.exceptions.SiteConfigurationException;
+import org.nrg.framework.services.ContextService;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
+import org.nrg.xdat.preferences.SiteConfigPreferences;
+import org.nrg.xdat.security.HistoricPasswordValidator;
+import org.nrg.xdat.security.PasswordValidatorChain;
+import org.nrg.xdat.security.RegExpValidator;
+import org.nrg.xdat.security.XDATUserMgmtServiceImpl;
+import org.nrg.xdat.security.services.UserManagementServiceI;
+import org.nrg.xdat.services.ThemeService;
+import org.nrg.xdat.services.impl.ThemeServiceImpl;
+import org.nrg.xnat.initialization.InitializingTasksExecutor;
+import org.nrg.xnat.restlet.XnatRestletExtensions;
+import org.nrg.xnat.restlet.actions.importer.ImporterHandlerPackages;
+import org.nrg.xnat.utils.XnatUserProvider;
+import org.springframework.context.annotation.*;
+
+import javax.inject.Inject;
+import java.util.Arrays;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.List;
+
+@Configuration
+@ComponentScan({"org.nrg.automation.repositories", "org.nrg.config.daos", "org.nrg.dcm.xnat", "org.nrg.dicomtools.filters",
+ "org.nrg.framework.datacache.impl.hibernate", "org.nrg.framework.services.impl", "org.nrg.notify.daos",
+ "org.nrg.prefs.repositories", "org.nrg.xdat.daos", "org.nrg.xdat.services.impl.hibernate", "org.nrg.xft.daos",
+ "org.nrg.xft.event.listeners", "org.nrg.xft.services", "org.nrg.xnat.configuration", "org.nrg.xnat.daos",
+ "org.nrg.xnat.event.listeners", "org.nrg.xnat.helpers.merge", "org.nrg.xnat.initialization.tasks",
+ "org.nrg.xnat.services", "org.nrg.xnat.services.impl.hibernate", "org.nrg.xnat.spawner.repositories"})
+@Import({FeaturesConfig.class, ReactorConfig.class})
+@ImportResource("WEB-INF/conf/mq-context.xml")
+public class ApplicationConfig {
+
+ @Bean
+ public ThemeService themeService() {
+ return new ThemeServiceImpl();
+ }
+
+ @Bean
+ @Primary
+ public ContextService contextService() {
+ return ContextService.getInstance();
+ }
+
+ @Bean
+ public InitializingTasksExecutor initializingTasksExecutor() {
+ return new InitializingTasksExecutor();
+ }
+
+ @Bean
+ public SiteConfigPreferences siteConfigPreferences() {
+ return new SiteConfigPreferences();
+ }
+
+ @Bean
+ public UserManagementServiceI userManagementService() {
+ // TODO: This should be made to use a preference setting.
+ return new XDATUserMgmtServiceImpl();
+ }
+
+ @Bean
+ public RegExpValidator regexValidator() throws SiteConfigurationException {
+ final String complexityExpression = _preferences.getPasswordComplexity();
+ final String complexityMessage = _preferences.getPasswordComplexityMessage();
+ return new RegExpValidator(complexityExpression, complexityMessage);
+ }
+
+ @Bean
+ public HistoricPasswordValidator historicPasswordValidator() throws SiteConfigurationException {
+ final int durationInDays = _preferences.getPasswordHistoryDuration();
+ return new HistoricPasswordValidator(durationInDays);
+ }
+
+ @Bean
+ public PasswordValidatorChain validator(final RegExpValidator regExpValidator, final HistoricPasswordValidator historicPasswordValidator) {
+ return new PasswordValidatorChain(Arrays.asList(regExpValidator, historicPasswordValidator));
+ }
+
+ // MIGRATION: I'm not even sure this is used, but we need to do away with it in favor of prefs.
+ @Bean
+ public List<String> propertiesRepositories() {
+ return Collections.singletonList("WEB-INF/conf/properties");
+ }
+
+ @Bean
+ public XnatUserProvider receivedFileUserProvider() throws SiteConfigurationException {
+ final String receivedFileUser = _preferences.getReceivedFileUser();
+ return new XnatUserProvider(receivedFileUser);
+ }
+
+ @Bean
+ public XnatRestletExtensions xnatRestletExtensions() {
+ return new XnatRestletExtensions(new HashSet<>(Arrays.asList(new String[]{"org.nrg.xnat.restlet.extensions"})));
+ }
+
+ @Bean
+ public ImporterHandlerPackages importerHandlerPackages() {
+ return new ImporterHandlerPackages(new HashSet<>(Arrays.asList(new String[]{"org.nrg.xnat.restlet.actions", "org.nrg.xnat.archive"})));
+ }
+
+ @Inject
+ private InitializerSiteConfiguration _preferences;
+}
diff --git a/src/main/java/org/nrg/xnat/configuration/ConfigResolver.java b/src/main/java/org/nrg/xnat/configuration/ConfigResolver.java
deleted file mode 100644
index 6af8f304..00000000
--- a/src/main/java/org/nrg/xnat/configuration/ConfigResolver.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package org.nrg.xnat.configuration;
-
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.stereotype.Component;
-
-import javax.annotation.Resource;
-import java.io.IOException;
-import java.io.InputStream;
-import java.nio.file.Files;
-import java.nio.file.Path;
-import java.nio.file.StandardOpenOption;
-import java.util.List;
-
-@Component
-public class ConfigResolver {
-
- public InputStream getConfigurationFile(final String name) throws IOException {
- for (final Path configFolder : _configFolderPaths) {
- final Path configFile = configFolder.resolve(name);
- if (_log.isDebugEnabled()) {
- _log.info("Searching for the configuration file {} in the path {}.", name, configFile.toString());
- }
- if (configFile.toFile().exists()) {
- if (_log.isInfoEnabled()) {
- _log.info("Found the configuration file {} in the path {}, returning.", name, configFile.toString());
- }
- return Files.newInputStream(configFile, StandardOpenOption.READ);
- }
- }
- if (_log.isDebugEnabled()) {
- _log.info("Found no configuration file named {} on any of the available configuration folders.");
- }
- return null;
- }
-
- private static final Logger _log = LoggerFactory.getLogger(ConfigResolver.class);
-
- @Resource(name="configFolderPaths")
- private List<Path> _configFolderPaths;
-}
diff --git a/src/main/java/org/nrg/xnat/configuration/FeaturesConfig.java b/src/main/java/org/nrg/xnat/configuration/FeaturesConfig.java
index 5ed2a0c8..450b4565 100644
--- a/src/main/java/org/nrg/xnat/configuration/FeaturesConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/FeaturesConfig.java
@@ -2,11 +2,11 @@ package org.nrg.xnat.configuration;
import org.apache.commons.lang3.StringUtils;
import org.nrg.config.exceptions.SiteConfigurationException;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.nrg.xdat.security.services.FeatureRepositoryServiceI;
import org.nrg.xdat.security.services.FeatureServiceI;
import org.nrg.xdat.security.services.RoleRepositoryServiceI;
import org.nrg.xdat.security.services.RoleServiceI;
-import org.nrg.xnat.initialization.InitializerSiteConfiguration;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.context.annotation.Bean;
@@ -14,14 +14,14 @@ import org.springframework.context.annotation.Configuration;
import javax.inject.Inject;
+import static org.nrg.xdat.security.services.FeatureRepositoryServiceI.DEFAULT_FEATURE_REPO_SERVICE;
+import static org.nrg.xdat.security.services.FeatureServiceI.DEFAULT_FEATURE_SERVICE;
+import static org.nrg.xdat.security.services.RoleRepositoryServiceI.DEFAULT_ROLE_REPO_SERVICE;
+import static org.nrg.xdat.security.services.RoleServiceI.DEFAULT_ROLE_SERVICE;
+
@Configuration
public class FeaturesConfig {
- public static final String DEFAULT_FEATURE_SERVICE = "org.nrg.xdat.security.services.impl.FeatureServiceImpl";
- public static final String DEFAULT_FEATURE_REPO_SERVICE = "org.nrg.xdat.security.services.impl.FeatureRepositoryServiceImpl";
- public static final String DEFAULT_ROLE_SERVICE = "org.nrg.xdat.security.services.impl.RoleServiceImpl";
- public static final String DEFAULT_ROLE_REPO_SERVICE = "org.nrg.xdat.security.services.impl.RoleRepositoryServiceImpl";
-
@Bean
public FeatureServiceI featureService() throws ClassNotFoundException, IllegalAccessException, InstantiationException, SiteConfigurationException {
final String serviceImpl = StringUtils.defaultIfBlank(_preferences.getFeatureService(), DEFAULT_FEATURE_SERVICE);
diff --git a/src/main/java/org/nrg/xnat/configuration/MqConfig.java b/src/main/java/org/nrg/xnat/configuration/MqConfig.java
new file mode 100644
index 00000000..993e9e95
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/configuration/MqConfig.java
@@ -0,0 +1,9 @@
+package org.nrg.xnat.configuration;
+
+import org.springframework.context.annotation.Configuration;
+// import org.springframework.jms.annotation.EnableJms;
+
+@Configuration
+// @EnableJms
+public class MqConfig {
+}
diff --git a/src/main/java/org/nrg/xnat/configuration/NotificationsConfig.java b/src/main/java/org/nrg/xnat/configuration/NotificationsConfig.java
index a132589a..41275904 100644
--- a/src/main/java/org/nrg/xnat/configuration/NotificationsConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/NotificationsConfig.java
@@ -6,7 +6,7 @@ import org.nrg.framework.orm.hibernate.HibernateEntityPackageList;
import org.nrg.notify.entities.ChannelRendererProvider;
import org.nrg.notify.renderers.ChannelRenderer;
import org.nrg.notify.renderers.NrgMailChannelRenderer;
-import org.nrg.xnat.initialization.InitializerSiteConfiguration;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
diff --git a/src/main/java/org/nrg/xnat/configuration/OrmConfig.java b/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
new file mode 100644
index 00000000..1e658387
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
@@ -0,0 +1,120 @@
+package org.nrg.xnat.configuration;
+
+import org.apache.commons.io.IOUtils;
+import org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory;
+import org.hibernate.cache.spi.RegionFactory;
+import org.hibernate.cfg.ImprovedNamingStrategy;
+import org.nrg.framework.exceptions.NrgServiceError;
+import org.nrg.framework.exceptions.NrgServiceException;
+import org.nrg.framework.orm.hibernate.PrefixedTableNamingStrategy;
+import org.nrg.framework.utilities.BasicXnatResourceLocator;
+import org.nrg.framework.utilities.Beans;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.config.PropertiesFactoryBean;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.core.env.Environment;
+import org.springframework.core.io.Resource;
+import org.springframework.orm.hibernate4.HibernateTransactionManager;
+import org.springframework.orm.hibernate4.LocalSessionFactoryBean;
+import org.springframework.transaction.PlatformTransactionManager;
+import org.springframework.transaction.annotation.EnableTransactionManagement;
+
+import javax.inject.Inject;
+import javax.sql.DataSource;
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+
+@Configuration
+@EnableTransactionManagement(proxyTargetClass = true)
+public class OrmConfig {
+ @Bean
+ public ImprovedNamingStrategy namingStrategy() {
+ return new PrefixedTableNamingStrategy("xhbm");
+ }
+
+ @Bean
+ public PropertiesFactoryBean hibernateProperties() {
+ final PropertiesFactoryBean bean = new PropertiesFactoryBean();
+ final Properties properties = Beans.getNamespacedProperties(_environment, "hibernate", false);
+ if (properties.size() == 0) {
+ if (_log.isDebugEnabled()) {
+ final StringBuilder message = new StringBuilder("No Hibernate properties specified, using default properties:\n");
+ for (final String property : DEFAULT_HIBERNATE_PROPERTIES.stringPropertyNames()) {
+ message.append(" * ").append(property).append(": ").append(DEFAULT_HIBERNATE_PROPERTIES.getProperty(property)).append("\n");
+ }
+ _log.debug(message.toString());
+ }
+ properties.putAll(DEFAULT_HIBERNATE_PROPERTIES);
+ }
+ bean.setProperties(properties);
+ return bean;
+ }
+
+ @Bean
+ public RegionFactory regionFactory() throws NrgServiceException {
+ try {
+ return new SingletonEhCacheRegionFactory(hibernateProperties().getObject());
+ } catch (IOException e) {
+ throw new NrgServiceException(NrgServiceError.Unknown, "An error occurred trying to retrieve the Hibernate properties", e);
+ }
+ }
+
+ @Bean
+ public LocalSessionFactoryBean sessionFactory(final DataSource dataSource) throws NrgServiceException {
+ try {
+ final LocalSessionFactoryBean bean = new LocalSessionFactoryBean();
+ final String[] packages = getXnatEntityPackages();
+ if (_log.isDebugEnabled()) {
+ final StringBuilder message = new StringBuilder("The following packages will be scanned for persistent entities:\n");
+ for (final String packageName : packages) {
+ message.append(" * ").append(packageName).append("\n");
+ }
+ _log.debug(message.toString());
+ }
+ bean.setPackagesToScan(packages);
+ bean.setDataSource(dataSource);
+ bean.setCacheRegionFactory(regionFactory());
+ bean.setHibernateProperties(hibernateProperties().getObject());
+ bean.setNamingStrategy(namingStrategy());
+ return bean;
+ } catch (IOException e) {
+ throw new NrgServiceException(NrgServiceError.Unknown, "An error occurred trying to retrieve the Hibernate properties", e);
+ }
+ }
+
+ @Bean
+ public PlatformTransactionManager transactionManager(final DataSource dataSource) throws NrgServiceException {
+ return new HibernateTransactionManager(sessionFactory(dataSource).getObject());
+ }
+
+ private static String[] getXnatEntityPackages() throws IOException {
+ final List<String> packages = new ArrayList<>();
+ for (final Resource resource : BasicXnatResourceLocator.getResources("classpath*:META-INF/xnat/entities/**/*-entity-packages.txt")) {
+ if (_log.isDebugEnabled()) {
+ _log.debug("Processing entity packages from the resource: " + resource.getFilename());
+ }
+ try (final InputStream input = resource.getInputStream()) {
+ packages.addAll(IOUtils.readLines(input, "UTF-8"));
+ }
+ }
+ return packages.toArray(new String[packages.size()]);
+ }
+
+ private static final Properties DEFAULT_HIBERNATE_PROPERTIES = new Properties() {{
+ setProperty("hibernate.dialect", "org.hibernate.dialect.PostgreSQL9Dialect");
+ setProperty("hibernate.hbm2ddl.auto", "update");
+ setProperty("hibernate.show_sql", "false");
+ setProperty("hibernate.cache.use_second_level_cache", "true");
+ setProperty("hibernate.cache.use_query_cache", "true");
+ }};
+
+ private static final Logger _log = LoggerFactory.getLogger(OrmConfig.class);
+
+ @Inject
+ private Environment _environment;
+}
diff --git a/src/main/java/org/nrg/xnat/configuration/PrearchiveConfig.java b/src/main/java/org/nrg/xnat/configuration/PrearchiveConfig.java
deleted file mode 100644
index 54129564..00000000
--- a/src/main/java/org/nrg/xnat/configuration/PrearchiveConfig.java
+++ /dev/null
@@ -1,15 +0,0 @@
-package org.nrg.xnat.configuration;
-
-import org.nrg.xnat.helpers.prearchive.PrearcConfig;
-import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.Configuration;
-
-@Configuration
-public class PrearchiveConfig {
- @Bean
- public PrearcConfig prearcConfig() {
- final PrearcConfig prearcConfig = new PrearcConfig();
- prearcConfig.setReloadPrearcDatabaseOnApplicationStartup(false);
- return prearcConfig;
- }
-}
diff --git a/src/main/java/org/nrg/xnat/configuration/PreferencesConfig.java b/src/main/java/org/nrg/xnat/configuration/PreferencesConfig.java
index 9fcf0b5e..7154bfe7 100644
--- a/src/main/java/org/nrg/xnat/configuration/PreferencesConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/PreferencesConfig.java
@@ -8,7 +8,7 @@ import org.nrg.config.services.impl.DefaultConfigService;
import org.nrg.config.services.impl.DefaultUserConfigurationService;
import org.nrg.prefs.configuration.NrgPrefsServiceConfiguration;
import org.nrg.prefs.services.PreferenceService;
-import org.nrg.xnat.initialization.InitializerSiteConfiguration;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.nrg.xnat.resolvers.XnatPreferenceEntityResolver;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
diff --git a/src/main/java/org/nrg/xnat/configuration/ReactorConfig.java b/src/main/java/org/nrg/xnat/configuration/ReactorConfig.java
index 50fa720b..f1581c29 100755
--- a/src/main/java/org/nrg/xnat/configuration/ReactorConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/ReactorConfig.java
@@ -1,18 +1,36 @@
package org.nrg.xnat.configuration;
+import org.nrg.xft.event.XftEventService;
+import org.nrg.xft.event.listeners.XftItemEventListener;
+import org.nrg.xnat.event.conf.EventPackages;
import org.springframework.context.annotation.Bean;
-import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
-
import reactor.Environment;
import reactor.bus.EventBus;
+import java.util.Arrays;
+import java.util.HashSet;
+
/**
* The Class ReactorConfig.
*/
@Configuration
-@ComponentScan({"org.nrg.xnat.event.listeners, org.nrg.xft.event, org.nrg.xft.event.listeners"})
public class ReactorConfig {
+ @Bean
+ public XftEventService xftEventService() {
+ return new XftEventService();
+ }
+
+ @Bean
+ public XftItemEventListener xftItemEventListener(final EventBus eventBus) {
+ return new XftItemEventListener(eventBus);
+ }
+
+ @Bean
+ public EventPackages eventPackages() {
+ // NOTE: These should be treated as parent packages. All sub-packages should be searched
+ return new EventPackages(new HashSet<>(Arrays.asList(new String[]{"org.nrg.xnat.event", "org.nrg.xft.event", "org.nrg.xdat.event"})));
+ }
/**
* Env.
@@ -20,20 +38,19 @@ public class ReactorConfig {
* @return the environment
*/
@Bean
- Environment env() {
- return Environment.initializeIfEmpty()
- .assignErrorJournal();
+ public Environment env() {
+ return Environment.initializeIfEmpty().assignErrorJournal();
}
/**
* Creates the event bus.
*
* @param env the env
+ *
* @return the event bus
*/
@Bean
- EventBus createEventBus(Environment env) {
- return EventBus.create(env, Environment.THREAD_POOL);
+ public EventBus createEventBus(Environment env) {
+ return EventBus.create(env, Environment.THREAD_POOL);
}
-
}
diff --git a/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java b/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
index d6715fc0..540fee31 100644
--- a/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
@@ -2,52 +2,58 @@ package org.nrg.xnat.configuration;
import org.nrg.config.exceptions.SiteConfigurationException;
import org.nrg.mail.services.EmailRequestLogService;
-import org.nrg.schedule.TriggerTaskProxy;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.nrg.xnat.helpers.prearchive.SessionXMLRebuilder;
-import org.nrg.xnat.initialization.InitializerSiteConfiguration;
import org.nrg.xnat.security.DisableInactiveUsers;
import org.nrg.xnat.security.ResetEmailRequests;
import org.nrg.xnat.security.ResetFailedLogins;
import org.nrg.xnat.security.alias.ClearExpiredAliasTokens;
import org.nrg.xnat.utils.XnatUserProvider;
+import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jms.core.JmsTemplate;
import org.springframework.scheduling.annotation.EnableScheduling;
import org.springframework.scheduling.annotation.SchedulingConfigurer;
import org.springframework.scheduling.concurrent.ThreadPoolTaskScheduler;
import org.springframework.scheduling.config.ScheduledTaskRegistrar;
+import org.springframework.scheduling.config.TriggerTask;
+import org.springframework.scheduling.support.CronTrigger;
+import org.springframework.scheduling.support.PeriodicTrigger;
import javax.inject.Inject;
-import javax.sql.DataSource;
import java.util.List;
@Configuration
@EnableScheduling
public class SchedulerConfig implements SchedulingConfigurer {
@Bean
- public TriggerTaskProxy disableInactiveUsers() throws SiteConfigurationException {
- return new TriggerTaskProxy(new DisableInactiveUsers(_preferences.getInactivityBeforeLockout()), _preferences.getInactivityBeforeLockoutSchedule());
+ public TriggerTask disableInactiveUsers() throws SiteConfigurationException {
+ return new TriggerTask(new DisableInactiveUsers(_preferences.getInactivityBeforeLockout()), new CronTrigger(_preferences.getInactivityBeforeLockoutSchedule()));
}
@Bean
- public TriggerTaskProxy resetFailedLogins() throws SiteConfigurationException {
- return new TriggerTaskProxy(new ResetFailedLogins(_dataSource), _preferences.getMaxFailedLoginsLockoutDuration());
+ public TriggerTask resetFailedLogins() throws SiteConfigurationException {
+ return new TriggerTask(new ResetFailedLogins(_template, _preferences.getMaxFailedLoginsLockoutDuration()), new PeriodicTrigger(900000));
}
@Bean
- public TriggerTaskProxy resetEmailRequests() {
- return new TriggerTaskProxy(new ResetEmailRequests(_emailRequestLogService), 900000);
+ public TriggerTask resetEmailRequests() {
+ return new TriggerTask(new ResetEmailRequests(_emailRequestLogService), new PeriodicTrigger(900000));
}
@Bean
- public TriggerTaskProxy clearExpiredAliasTokens() throws SiteConfigurationException {
- return new TriggerTaskProxy(new ClearExpiredAliasTokens(_dataSource, _preferences.getAliasTokenTimeout()), 3600000);
+ public TriggerTask clearExpiredAliasTokens() throws SiteConfigurationException {
+ return new TriggerTask(new ClearExpiredAliasTokens(_template, _preferences.getAliasTokenTimeout()), new PeriodicTrigger(3600000));
}
@Bean
- public TriggerTaskProxy rebuildSessionéXmls() throws SiteConfigurationException {
- return new TriggerTaskProxy(new SessionXMLRebuilder(_provider, _preferences.getSessionXmlRebuilderInterval(), _jmsTemplate), _preferences.getSessionXmlRebuilderRepeat(), 60000);
+ public TriggerTask rebuildSessionXmls() throws SiteConfigurationException {
+ final PeriodicTrigger trigger = new PeriodicTrigger(_preferences.getSessionXmlRebuilderRepeat());
+ trigger.setInitialDelay(60000);
+ return new TriggerTask(new SessionXMLRebuilder(_provider, _preferences.getSessionXmlRebuilderInterval(), _jmsTemplate), trigger);
}
@Bean(destroyMethod = "shutdown")
@@ -63,17 +69,18 @@ public class SchedulerConfig implements SchedulingConfigurer {
// taskRegistrar.addTriggerTask(resetEmailRequests());
// taskRegistrar.addTriggerTask(clearExpiredAliasTokens());
// taskRegistrar.addTriggerTask(rebuildSessionXmls());
- for (final TriggerTaskProxy triggerTask : _triggerTasks) {
+ for (final TriggerTask triggerTask : _triggerTasks) {
taskRegistrar.addTriggerTask(triggerTask);
}
}
- @Inject
- private DataSource _dataSource;
-
@Inject
private EmailRequestLogService _emailRequestLogService;
+ @Autowired
+ @Lazy
+ private JdbcTemplate _template;
+
@Inject
private XnatUserProvider _provider;
@@ -85,5 +92,5 @@ public class SchedulerConfig implements SchedulingConfigurer {
@SuppressWarnings("MismatchedQueryAndUpdateOfCollection")
@Inject
- private List<TriggerTaskProxy> _triggerTasks;
+ private List<TriggerTask> _triggerTasks;
}
\ No newline at end of file
diff --git a/src/main/java/org/nrg/xnat/configuration/SiteConfigPreferences.java b/src/main/java/org/nrg/xnat/configuration/SiteConfigPreferences.java
deleted file mode 100644
index afe93e53..00000000
--- a/src/main/java/org/nrg/xnat/configuration/SiteConfigPreferences.java
+++ /dev/null
@@ -1,881 +0,0 @@
-package org.nrg.xnat.configuration;
-
-import org.nrg.prefs.annotations.NrgPreference;
-import org.nrg.prefs.annotations.NrgPreferenceBean;
-import org.nrg.prefs.beans.AbstractPreferenceBean;
-import org.nrg.prefs.exceptions.InvalidPreferenceName;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.util.Date;
-import java.util.List;
-import java.util.Map;
-
-@NrgPreferenceBean(toolId = SiteConfigPreferences.SITE_CONFIG_TOOL_ID,
- toolName = "XNAT Site Preferences",
- description = "Manages site configurations and settings for the XNAT system.",
-
- strict = false)
-public class SiteConfigPreferences extends AbstractPreferenceBean {
- public static final String SITE_CONFIG_TOOL_ID = "siteConfig";
-
- @NrgPreference(defaultValue = "XNAT")
- public String getSiteTitle() {
- return getValue("siteTitle");
- }
-
- public void setSiteTitle(final String siteTitle) {
- try {
- set(siteTitle, "siteTitle");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name siteTitle: something is very wrong here.", e);
- }
- }
-
- @NrgPreference
- public String getSiteUrl() {
- return getValue("siteUrl");
- }
-
- public void setSiteUrl(final String siteUrl) {
- try {
- set(siteUrl, "siteUrl");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name siteUrl: something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "you@yoursite.org")
- public String getAdminEmail() {
- return getValue("adminEmail");
- }
-
- public void setAdminEmail(final String adminEmail) {
- try {
- set(adminEmail, "adminEmail");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'adminEmail': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/data/xnat/archive")
- public String getArchiveRootPath() {
- return getValue("archiveRootPath");
- }
-
- public void setArchiveRootPath(final String archiveRootPath) {
- try {
- set(archiveRootPath, "archiveRootPath");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'archiveRootPath': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/data/xnat/prearchive")
- public String getPrearchivePath() {
- return getValue("prearchivePath");
- }
-
- public void setPrearchivePath(final String prearchivePath) {
- try {
- set(prearchivePath, "prearchivePath");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'prearchivePath': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/data/xnat/cache")
- public String getCachePath() {
- return getValue("cachePath");
- }
-
- public void setCachePath(final String cachePath) {
- try {
- set(cachePath, "cachePath");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'cachePath': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/data/xnat/ftp")
- public String getFtpPath() {
- return getValue("ftpPath");
- }
-
- public void setFtpPath(final String ftpPath) {
- try {
- set(ftpPath, "ftpPath");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'ftpPath': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/data/xnat/build")
- public String getBuildPath() {
- return getValue("buildPath");
- }
-
- public void setBuildPath(final String buildPath) {
- try {
- set(buildPath, "buildPath");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'buildPath': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/data/xnat/pipeline")
- public String getPipelinePath() {
- return getValue("pipelinePath");
- }
-
- public void setPipelinePath(final String pipelinePath) {
- try {
- set(pipelinePath, "pipelinePath");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'pipelinePath': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "{'host':'mail.server','port':'25'}")
- public Map<String, String> getSmtpServer() {
- return getMapValue("smtpServer");
- }
-
- public void setSmtpServer(final Map<String, String> smtpServer) {
- try {
- setMapValue("smtpServer", smtpServer);
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'smtpServer': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "^.*$")
- public String getPasswordComplexity() {
- return getValue("passwordComplexity");
- }
-
- public void setPasswordComplexity(final String passwordComplexity) {
- try {
- set(passwordComplexity, "passwordComplexity");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'passwordComplexity': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "Password is not sufficiently complex.")
- public String getPasswordComplexityMessage() {
- return getValue("passwordComplexityMessage");
- }
-
- public void setPasswordComplexityMessage(final String passwordComplexityMessage) {
- try {
- set(passwordComplexityMessage, "passwordComplexityMessage");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'passwordComplexityMessage': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "365")
- public int getPasswordHistoryDuration() {
- return getIntegerValue("passwordHistoryDuration");
- }
-
- public void setPasswordHistoryDuration(final int passwordHistoryDuration) {
- try {
- setIntegerValue(passwordHistoryDuration, "passwordHistoryDuration");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'passwordHistoryDuration': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true")
- public boolean getRequireLogin() {
- return getBooleanValue("requireLogin");
- }
-
- public void setRequireLogin(final boolean requireLogin) {
- try {
- setBooleanValue(requireLogin, "requireLogin");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'requireLogin': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "false")
- public boolean getUserRegistration() {
- return getBooleanValue("userRegistration");
- }
-
- public void setUserRegistration(final boolean userRegistration) {
- try {
- setBooleanValue(userRegistration, "userRegistration");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'userRegistration': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true")
- public boolean getEmailVerification() {
- return getBooleanValue("emailVerification");
- }
-
- public void setEmailVerification(final boolean emailVerification) {
- try {
- setBooleanValue(emailVerification, "emailVerification");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'emailVerification': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true")
- public boolean getEnableCsrfToken() {
- return getBooleanValue("enableCsrfToken");
- }
-
- public void setEnableCsrfToken(final boolean enableCsrfToken) {
- try {
- setBooleanValue(enableCsrfToken, "enableCsrfToken");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'enableCsrfToken': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "false")
- public boolean getRestrictUserListAccessToAdmins() {
- return getBooleanValue("restrictUserListAccessToAdmins");
- }
-
- public void setRestrictUserListAccessToAdmins(final boolean restrictUserListAccessToAdmins) {
- try {
- setBooleanValue(restrictUserListAccessToAdmins, "restrictUserListAccessToAdmins");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'restrictUserListAccessToAdmins': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true")
- public boolean getRequireSaltedPasswords() {
- return getBooleanValue("requireSaltedPasswords");
- }
-
- public void setRequireSaltedPasswords(final boolean requireSaltedPasswords) {
- try {
- setBooleanValue(requireSaltedPasswords, "requireSaltedPasswords");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'requireSaltedPasswords': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true")
- public boolean getEmailAllowNonuserSubscribers() {
- return getBooleanValue("emailAllowNonuserSubscribers");
- }
-
- public void setEmailAllowNonuserSubscribers(final boolean emailAllowNonuserSubscribers) {
- try {
- setBooleanValue(emailAllowNonuserSubscribers, "emailAllowNonuserSubscribers");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'emailAllowNonuserSubscribers': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "Interval")
- public String getPasswordExpirationType() {
- return getValue("passwordExpirationType");
- }
-
- public void setPasswordExpirationType(final String passwordExpirationType) {
- try {
- set(passwordExpirationType, "passwordExpirationType");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'passwordExpirationType': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "365")
- public int getPasswordExpirationInterval() {
- return getIntegerValue("passwordExpirationInterval");
- }
-
- public void setPasswordExpirationInterval(final int passwordExpirationInterval) {
- try {
- setIntegerValue(passwordExpirationInterval, "passwordExpirationInterval");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'passwordExpirationInterval': something is very wrong here.", e);
- }
- }
-
- @NrgPreference
- public Date getPasswordExpirationDate() {
- return getDateValue("passwordExpirationDate");
- }
-
- public void setPasswordExpirationDate(final Date passwordExpirationDate) {
- try {
- setDateValue(passwordExpirationDate, "passwordExpirationDate");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'passwordExpirationDate': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "false")
- public boolean getShowApplet() {
- return getBooleanValue("showApplet");
- }
-
- public void setShowApplet(final boolean showApplet) {
- try {
- setBooleanValue(showApplet, "showApplet");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'showApplet': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "false")
- public boolean getEnableProjectAppletScript() {
- return getBooleanValue("enableProjectAppletScript");
- }
-
- public void setEnableProjectAppletScript(final boolean enableProjectAppletScript) {
- try {
- setBooleanValue(enableProjectAppletScript, "enableProjectAppletScript");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'enableProjectAppletScript': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true")
- public boolean getChecksums() {
- return getBooleanValue("checksums");
- }
-
- public void setChecksums(final boolean checksums) {
- try {
- setBooleanValue(checksums, "checksums");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'checksums': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true")
- public boolean getScanTypeMapping() {
- return getBooleanValue("scanTypeMapping");
- }
-
- public void setScanTypeMapping(final boolean scanTypeMapping) {
- try {
- setBooleanValue(scanTypeMapping, "scanTypeMapping");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'scanTypeMapping': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "org.nrg.xnat.utils.ChecksumsSiteConfigurationListener", property = "checksums.property.changed.listener")
- public String getChecksumsPropertyChangedListener() {
- return getValue("checksums.property.changed.listener");
- }
-
- public void setChecksumsPropertyChangedListener(final String checksumsPropertyChangedListener) {
- try {
- set(checksumsPropertyChangedListener, "checksums.property.changed.listener");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'checksums.property.changed.listener': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true")
- public boolean isEnableDicomReceiver() {
- return getBooleanValue("enableDicomReceiver");
- }
-
- public void setEnableDicomReceiver(final boolean enableDicomReceiver) {
- try {
- setBooleanValue(enableDicomReceiver, "enableDicomReceiver");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'enableDicomReceiver': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "org.nrg.dcm.DicomSCPSiteConfigurationListener", property = "enableDicomReceiver.property.changed.listener")
- public String getEnableDicomReceiverPropertyChangedListener() {
- return getValue("enableDicomReceiver.property.changed.listener");
- }
-
- public void setEnableDicomReceiverPropertyChangedListener(final String enableDicomReceiverPropertyChangedListener) {
- try {
- set(enableDicomReceiverPropertyChangedListener, "enableDicomReceiver.property.changed.listener");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'enableDicomReceiver.property.changed.listener': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "admin")
- public String getReceivedFileUser() {
- return getValue("receivedFileUser");
- }
-
- public void setReceivedFileUser(final String receivedFileUser) {
- try {
- set(receivedFileUser, "receivedFileUser");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'receivedFileUser': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "Session", property = "displayNameForGenericImageSession.singular")
- public String getImageSessionDisplayNameSingular() {
- return getValue("displayNameForGenericImageSession.singular");
- }
-
- public void setImageSessionDisplayNameSingular(final String displayNameForGenericImageSessionSingular) {
- try {
- set(displayNameForGenericImageSessionSingular, "displayNameForGenericImageSession.singular");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'displayNameForGenericImageSession.singular': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "Sessions", property = "displayNameForGenericImageSession.plural")
- public String getImageSessionDisplayNamePlural() {
- return getValue("displayNameForGenericImageSession.plural");
- }
-
- public void setImageSessionDisplayNamePlural(final String displayNameForGenericImageSessionPlural) {
- try {
- set(displayNameForGenericImageSessionPlural, "displayNameForGenericImageSession.plural");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'displayNameForGenericImageSession.plural': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "['zip','jar','rar','ear','gar','mrb']")
- public List<String> getZipExtensions() {
- return getListValue("zipExtensions");
- }
-
- public void setZipExtensions(final List<String> zipExtensions) {
- try {
- setListValue("zipExtensions", zipExtensions);
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'zipExtensions': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "Page")
- public String getSiteDescriptionType() {
- return getValue("siteDescriptionType");
- }
-
- public void setSiteDescriptionType(final String siteDescriptionType) {
- try {
- set(siteDescriptionType, "siteDescriptionType");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'siteDescriptionType': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/screens/site_description.vm")
- public String getSiteDescriptionPage() {
- return getValue("siteDescriptionPage");
- }
-
- public void setSiteDescriptionPage(final String siteDescriptionPage) {
- try {
- set(siteDescriptionPage, "siteDescriptionPage");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'siteDescriptionPage': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "SITE DESCRIPTION HERE: Go to Administer -> Configuration -> Site Information to change.")
- public String getSiteDescriptionText() {
- return getValue("siteDescriptionText");
- }
-
- public void setSiteDescriptionText(final String siteDescriptionText) {
- try {
- set(siteDescriptionText, "siteDescriptionText");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'siteDescriptionText': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/screens/QuickSearch.vm")
- public String getSiteLoginLanding() {
- return getValue("siteLoginLanding");
- }
-
- public void setSiteLoginLanding(final String siteLoginLanding) {
- try {
- set(siteLoginLanding, "siteLoginLanding");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'siteLoginLanding': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/Index.vm")
- public String getSiteLandingLayout() {
- return getValue("siteLandingLayout");
- }
-
- public void setSiteLandingLayout(final String siteLandingLayout) {
- try {
- set(siteLandingLayout, "siteLandingLayout");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'siteLandingLayout': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/screens/QuickSearch.vm")
- public String getSiteHome() {
- return getValue("siteHome");
- }
-
- public void setSiteHome(final String siteHome) {
- try {
- set(siteHome, "siteHome");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'siteHome': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "/Index.vm")
- public String getSiteHomeLayout() {
- return getValue("siteHomeLayout");
- }
-
- public void setSiteHomeLayout(final String siteHomeLayout) {
- try {
- set(siteHomeLayout, "siteHomeLayout");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'siteHomeLayout': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "false", property = "UI.debug-extension-points")
- public boolean getUiDebugExtensionPoints() {
- return getBooleanValue("UI.debug-extension-points");
- }
-
- public void setUiDebugExtensionPoints(final boolean uiDebugExtensionPoints) {
- try {
- setBooleanValue(uiDebugExtensionPoints, "UI.debug-extension-points");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.debug-extension-points': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.allow-advanced-search")
- public boolean getUiAllowAdvancedSearch() {
- return getBooleanValue("UI.allow-advanced-search");
- }
-
- public void setuiAllowAdvancedSearch(final boolean uiAllowAdvancedSearch) {
- try {
- setBooleanValue(uiAllowAdvancedSearch, "UI.allow-advanced-search");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.allow-advanced-search': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.allow-new-user-comments")
- public boolean getUiAllowNewUserComments() {
- return getBooleanValue("UI.allow-new-user-comments");
- }
-
- public void setUiAllowNewUserComments(final boolean uiAllowNewUserComments) {
- try {
- setBooleanValue(uiAllowNewUserComments, "UI.allow-new-user-comments");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.allow-new-user-comments': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.allow-scan-addition")
- public boolean getUiAllowScanAddition() {
- return getBooleanValue("UI.allow-scan-addition");
- }
-
- public void setUiAllowScanAddition(final boolean uiAllowScanAddition) {
- try {
- setBooleanValue(uiAllowScanAddition, "UI.allow-scan-addition");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.allow-scan-addition': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.show-left-bar")
- public boolean getUiShowLeftBar() {
- return getBooleanValue("UI.show-left-bar");
- }
-
- public void setUiShowLeftBar(final boolean uiShowLeftBar) {
- try {
- setBooleanValue(uiShowLeftBar, "UI.show-left-bar");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.show-left-bar': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.show-left-bar-projects")
- public boolean getUiShowLeftBarProjects() {
- return getBooleanValue("UI.show-left-bar-projects");
- }
-
- public void setUiShowLeftBarProjects(final boolean uiShowLeftBarProjects) {
- try {
- setBooleanValue(uiShowLeftBarProjects, "UI.show-left-bar-projects");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.show-left-bar-projects': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.show-left-bar-favorites")
- public boolean getUiShowLeftBarFavorites() {
- return getBooleanValue("UI.show-left-bar-favorites");
- }
-
- public void setUiShowLeftBarFavorites(final boolean uiShowLeftBarFavorites) {
- try {
- setBooleanValue(uiShowLeftBarFavorites, "UI.show-left-bar-favorites");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.show-left-bar-favorites': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.show-left-bar-search")
- public boolean getUiShowLeftBarSearch() {
- return getBooleanValue("UI.show-left-bar-search");
- }
-
- public void setUiShowLeftBarSearch(final boolean uiShowLeftBarSearch) {
- try {
- setBooleanValue(uiShowLeftBarSearch, "UI.show-left-bar-search");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.show-left-bar-search': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.show-left-bar-browse")
- public boolean getUiShowLeftBarBrowse() {
- return getBooleanValue("UI.show-left-bar-browse");
- }
-
- public void setUiShowLeftBarBrowse(final boolean uiShowLeftBarBrowse) {
- try {
- setBooleanValue(uiShowLeftBarBrowse, "UI.show-left-bar-browse");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.show-left-bar-browse': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.show-manage-files")
- public boolean getUiShowManageFiles() {
- return getBooleanValue("UI.show-manage-files");
- }
-
- public void setUiShowManageFiles(final boolean uiShowManageFiles) {
- try {
- setBooleanValue(uiShowManageFiles, "UI.show-manage-files");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.show-manage-files': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "true", property = "UI.allow-non-admin-project-creation")
- public boolean getUiAllowNonAdminProjectCreation() {
- return getBooleanValue("UI.allow-non-admin-project-creation");
- }
-
- public void setUiAllowNonAdminProjectCreation(final boolean uiAllowNonAdminProjectCreation) {
- try {
- setBooleanValue(uiAllowNonAdminProjectCreation, "UI.allow-non-admin-project-creation");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.allow-non-admin-project-creation': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "Your login attempt failed because the username and password combination you provided was invalid. After %d failed login attempts, your user account will be locked. If you believe your account is currently locked, you can:<ul><li>Unlock it by resetting your password</li><li>Wait one hour for it to unlock automatically</li></ul>", property = "UI.login_failure_message")
- public String getUiLogin_failure_message() {
- return getValue("UI.login_failure_message");
- }
-
- public void setUiLoginFailureMessage(final String uiLoginFailureMessage) {
- try {
- set(uiLoginFailureMessage, "UI.login_failure_message");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.login_failure_message': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "false", property = "UI.allow-blocked-subject-assessor-view")
- public boolean getUiAllowBlockedSubjectAssessorView() {
- return getBooleanValue("UI.allow-blocked-subject-assessor-view");
- }
-
- public void setUiAllowBlockedSubjectAssessorView(final boolean uiAllowBlockedSubjectAssessorView) {
- try {
- setBooleanValue(uiAllowBlockedSubjectAssessorView, "UI.allow-blocked-subject-assessor-view");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'UI.allow-blocked-subject-assessor-view': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = FeaturesConfig.DEFAULT_FEATURE_SERVICE, property = "security.services.feature.default")
- public String getFeatureService() {
- return getValue("security.services.feature.default");
- }
-
- public void setFeatureService(final String featureService) {
- try {
- set(featureService, "security.services.feature.default");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'security.services.feature.default': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = FeaturesConfig.DEFAULT_FEATURE_REPO_SERVICE, property = "security.services.featureRepository.default")
- public String getFeatureRepositoryService() {
- return getValue("security.services.featureRepository.default");
- }
-
- public void setFeatureRepositoryService(final String featureRepositoryService) {
- try {
- set(featureRepositoryService, "security.services.featureRepository.default");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'security.services.featureRepository.default': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = FeaturesConfig.DEFAULT_ROLE_SERVICE, property = "security.services.role.default")
- public String getRoleService() {
- return getValue("security.services.role.default");
- }
-
- public void setRoleService(final String roleService) {
- try {
- set(roleService, "security.services.role.default");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'security.services.role.default': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = FeaturesConfig.DEFAULT_ROLE_REPO_SERVICE, property = "security.services.roleRepository.default")
- public String getRoleRepositoryService() {
- return getValue("security.services.roleRepository.default");
- }
-
- public void setRoleRepositoryService(final String roleRepositoryService) {
- try {
- set(roleRepositoryService, "security.services.roleRepository.default");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'security.services.roleRepository.default': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "XNAT")
- public String getEmailPrefix() {
- return getValue("emailPrefix");
- }
-
- public void setEmailPrefix(final String emailPrefix) {
- try {
- set(emailPrefix, "emailPrefix");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'emailPrefix': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "org.nrg.config.services.impl.PrefsBasedSiteConfigurationService", property = "admin.siteConfig.service")
- public String getSiteConfigurationService() {
- return getValue("admin.siteConfig.service");
- }
-
- public void setSiteConfigurationService(final String siteConfigurationService) {
- try {
- set(siteConfigurationService, "admin.siteConfig.service");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'admin.siteConfig.service': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "86400000")
- public int getMaxFailedLoginsLockoutDuration() {
- return getIntegerValue("maxFailedLoginsLockoutDuration");
- }
-
- public void setMaxFailedLoginsLockoutDuration(final int maxFailedLoginsLockoutDuration) {
- try {
- setIntegerValue(maxFailedLoginsLockoutDuration, "maxFailedLoginsLockoutDuration");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'maxFailedLoginsLockoutDuration': something is very wrong here.", e);
- }
- }
-
- private static final Logger _log = LoggerFactory.getLogger(SiteConfigPreferences.class);
-
- @NrgPreference(defaultValue = "31556926")
- public int getInactivityBeforeLockout() {
- return getIntegerValue("inactivityBeforeLockout");
- }
-
- public void setInactivityBeforeLockout(final int inactivityBeforeLockout) {
- try {
- setIntegerValue(inactivityBeforeLockout, "inactivityBeforeLockout");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'inactivityBeforeLockout': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "0 0 1 * * ?")
- public String getInactivityBeforeLockoutSchedule() {
- return getValue("inactivityBeforeLockoutSchedule");
- }
-
- public void setInactivityBeforeLockoutSchedule(final String inactivityBeforeLockoutSchedule) {
- try {
- set(inactivityBeforeLockoutSchedule, "inactivityBeforeLockoutSchedule");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'inactivityBeforeLockoutSchedule': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "60000")
- public long getSessionXmlRebuilderRepeat() {
- return getLongValue("sessionXmlRebuilderRepeat");
- }
-
- public void setSessionXmlRebuilderRepeat(final long sessionXmlRebuilderRepeat) {
- try {
- setLongValue(sessionXmlRebuilderRepeat, "sessionXmlRebuilderRepeat");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'sessionXmlRebuilderRepeat': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "5")
- public int getSessionXmlRebuilderInterval() {
- return getIntegerValue("sessionXmlRebuilderInterval");
- }
-
- public void setSessionXmlRebuilderInterval(final int sessionXmlRebuilderInterval) {
- try {
- setIntegerValue(sessionXmlRebuilderInterval, "sessionXmlRebuilderInterval");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'sessionXmlRebuilderInterval': something is very wrong here.", e);
- }
- }
-
- @NrgPreference(defaultValue = "2 days")
- public String getAliasTokenTimeout() {
- return getValue("aliasTokenTimeout");
- }
-
- public void setAliasTokenTimeout(final String aliasTokenTimeout) {
- try {
- set(aliasTokenTimeout, "aliasTokenTimeout");
- } catch (InvalidPreferenceName e) {
- _log.error("Invalid preference name 'aliasTokenTimeout': something is very wrong here.", e);
- }
- }
-}
diff --git a/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java b/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java
index a9267f8b..ea599485 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/AutomationEventScriptHandler.java
@@ -3,6 +3,7 @@ package org.nrg.xnat.event.listeners;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import org.apache.commons.lang3.StringUtils;
+import org.hibernate.exception.ConstraintViolationException;
import org.nrg.automation.entities.Script;
import org.nrg.automation.entities.ScriptOutput;
import org.nrg.automation.entities.ScriptOutput.Status;
@@ -11,13 +12,12 @@ import org.nrg.automation.services.ScriptTriggerService;
import org.nrg.automation.services.impl.hibernate.HibernateScriptTriggerService;
import org.nrg.framework.constants.Scope;
import org.nrg.framework.exceptions.NrgServiceException;
-import org.nrg.xdat.XDAT;
import org.nrg.xdat.security.helpers.Users;
import org.nrg.xdat.security.user.exceptions.UserInitException;
import org.nrg.xdat.security.user.exceptions.UserNotFoundException;
-import org.nrg.xdat.services.impl.hibernate.HibernateAutomationEventIdsService;
-import org.nrg.xdat.services.impl.hibernate.HibernateAutomationFiltersService;
-import org.nrg.xdat.services.impl.hibernate.HibernatePersistentEventService;
+import org.nrg.xdat.services.AutomationEventIdsService;
+import org.nrg.xdat.services.AutomationFiltersService;
+import org.nrg.xdat.services.PersistentEventService;
import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xft.event.AutomationEventImplementerI;
import org.nrg.xft.event.EventUtils;
@@ -35,6 +35,8 @@ import org.nrg.xnat.services.messaging.automation.AutomatedScriptRequest;
import org.nrg.xnat.utils.WorkflowUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jdbc.core.RowMapper;
import org.springframework.stereotype.Service;
@@ -61,79 +63,107 @@ import static reactor.bus.selector.Selectors.type;
@Service
@SuppressWarnings("unused")
public class AutomationEventScriptHandler implements Consumer<Event<AutomationEventImplementerI>> {
-
- private String EMAIL_SUBJECT = "Automation Results";
-
- /** The Constant logger. */
+
+ /**
+ * The Constant logger.
+ */
private static final Logger logger = LoggerFactory.getLogger(AutomationEventScriptHandler.class);
-
- /** The _service. */
- @Inject ScriptRunnerService _service;
-
- /** The _script trigger service. */
- @Inject ScriptTriggerService _scriptTriggerService;
-
- /** The _data source. */
- @Inject DataSource _dataSource;
-
- /**
- * Instantiates a new automated script handler.
- *
- * @param eventBus the event bus
- */
- @Inject public AutomationEventScriptHandler( EventBus eventBus ){
- eventBus.on(type(AutomationEventImplementerI.class), this);
- }
-
- /**
- * init - update xhbm_script_trigger table for XNAT 1.7
- */
- @PostConstruct
- public void initUpdateTables() {
- /** Update script trigger table for XNAT 1.7. Drop constraints on any columns other than id and trigger_id */
+
+ /**
+ * The _service.
+ */
+ @Autowired
+ @Lazy
+ private ScriptRunnerService _service;
+
+ /**
+ * The _script trigger service.
+ */
+ @Autowired
+ @Lazy
+ private ScriptTriggerService _scriptTriggerService;
+
+ /**
+ * The _data source.
+ */
+ @Inject
+ private DataSource _dataSource;
+
+ /**
+ * Automation filters service.
+ */
+ @Inject
+ private AutomationFiltersService _filtersService;
+
+ /**
+ * Persistent event service.
+ */
+ @Inject
+ private PersistentEventService _persistentEventService;
+
+ /**
+ * Automation event IDs service.
+ */
+ @Inject
+ private AutomationEventIdsService _idsService;
+
+ /**
+ * Instantiates a new automated script handler.
+ *
+ * @param eventBus the event bus
+ */
+ @Inject
+ public AutomationEventScriptHandler(EventBus eventBus) {
+ eventBus.on(type(AutomationEventImplementerI.class), this);
+ }
+
+ /**
+ * init - update xhbm_script_trigger table for XNAT 1.7
+ */
+ @PostConstruct
+ public void initUpdateTables() {
+ /** Update script trigger table for XNAT 1.7. Drop constraints on any columns other than id and trigger_id */
if (_scriptTriggerService instanceof HibernateScriptTriggerService) {
-
+
List<String> cleanUpQuery = (new JdbcTemplate(_dataSource)).query(
- "SELECT DISTINCT 'ALTER TABLE '||tc.table_name||' DROP CONSTRAINT '||tc.constraint_name||';'" +
- " FROM information_schema.table_constraints tc " +
- " LEFT JOIN information_schema.constraint_column_usage cu " +
- " ON cu.constraint_name = tc.constraint_name " +
- " WHERE (tc.table_name='xhbm_script_trigger' AND cu.column_name NOT IN ('id', 'trigger_id')) "
- , new RowMapper<String>() {
- public String mapRow(ResultSet rs, int rowNum) throws SQLException {
- return rs.getString(1);
- }
- });
+ "SELECT DISTINCT 'ALTER TABLE '||tc.table_name||' DROP CONSTRAINT '||tc.constraint_name||';'" +
+ " FROM information_schema.table_constraints tc " +
+ " LEFT JOIN information_schema.constraint_column_usage cu " +
+ " ON cu.constraint_name = tc.constraint_name " +
+ " WHERE (tc.table_name='xhbm_script_trigger' AND cu.column_name NOT IN ('id', 'trigger_id')) "
+ , new RowMapper<String>() {
+ public String mapRow(ResultSet rs, int rowNum) throws SQLException {
+ return rs.getString(1);
+ }
+ });
if (!cleanUpQuery.isEmpty()) {
- logger.info("Cleaning up pre XNAT 1.7 constraints on the xhbm_script_trigger and xhbm_event tables");
- for (String query : cleanUpQuery) {
- if (query.contains("xhbm_script_trigger")) {
- logger.info("Execute clean-up query (" + query + ")");
- new JdbcTemplate(_dataSource).execute(query);
- }
- }
+ logger.info("Cleaning up pre XNAT 1.7 constraints on the xhbm_script_trigger and xhbm_event tables");
+ for (String query : cleanUpQuery) {
+ if (query.contains("xhbm_script_trigger")) {
+ logger.info("Execute clean-up query (" + query + ")");
+ new JdbcTemplate(_dataSource).execute(query);
+ }
+ }
}
/** Update table rows for pre-XNAT 1.7 tables to fill in missing column values with defaults */
- ((HibernateScriptTriggerService)_scriptTriggerService).updateOldStyleScriptTriggers();
+ ((HibernateScriptTriggerService) _scriptTriggerService).updateOldStyleScriptTriggers();
+ }
+ }
+
+ /* (non-Javadoc)
+ * @see reactor.fn.Consumer#accept(java.lang.Object)
+ */
+ @Override
+ public void accept(Event<AutomationEventImplementerI> event) {
+ try {
+ handleAsPersistentEventIfMarkedPersistent(event);
+ updateAutomationTables(event);
+ } catch (Throwable t) {
+ logger.error("Unexpected error persisting Persistent/Automation event information", t);
+ } finally {
+ handleEvent(event);
}
- }
-
- /* (non-Javadoc)
- * @see reactor.fn.Consumer#accept(java.lang.Object)
- */
- @Override
- public void accept(Event<AutomationEventImplementerI> event) {
-
- try {
- handleAsPersistentEventIfMarkedPersistent(event);
- updateAutomationTables(event);
- } catch (Throwable t) {
- logger.error("Unexpected error persisting Persistent/Automation event information",t);
- } finally {
- handleEvent(event);
- }
-
- }
+ }
/**
* Update automation tables.
@@ -141,124 +171,121 @@ public class AutomationEventScriptHandler implements Consumer<Event<AutomationEv
* @param event the event
*/
private void updateAutomationTables(Event<AutomationEventImplementerI> event) {
- final HibernateAutomationEventIdsService idsService = XDAT.getContextService().getBean(HibernateAutomationEventIdsService.class);
- final AutomationEventImplementerI eventData = event.getData();
- if (eventData.getEventId()==null || eventData.getClass()==null) {
- return;
- }
- List<AutomationEventIds> autoIds = idsService.getEventIds(eventData.getExternalId(), eventData.getSrcEventClass(), true);
- if (autoIds.size()<1) {
- final AutomationEventIds ids = new AutomationEventIds(eventData);
- idsService.saveOrUpdate(ids);
- } else {
- for (final AutomationEventIds ids : autoIds) {
- if (!ids.getEventIds().contains(eventData.getEventId())) {
- ids.getEventIds().add(eventData.getEventId());
- idsService.saveOrUpdate(ids);
- }
- }
- }
- final HibernateAutomationFiltersService filtersService = XDAT.getContextService().getBean(HibernateAutomationFiltersService.class);
- final Class<? extends AutomationEventImplementerI> clazz = eventData.getClass();
- for (final Method method : Arrays.asList(clazz.getMethods())) {
- if (method.isAnnotationPresent(Filterable.class) && method.getName().substring(0,3).equalsIgnoreCase("get")) {
- final char c[] = method.getName().substring(3).toCharArray();
- c[0] = Character.toLowerCase(c[0]);
- final String column = new String(c);
- AutomationFilters filters = filtersService.getAutomationFilters(eventData.getExternalId(), eventData.getSrcEventClass(), column, true);
- if (filters == null) {
- filters = new AutomationFilters(eventData, column);
- filtersService.saveOrUpdate(filters);
- } else {
- try {
- final String value = method.invoke(eventData).toString();
- final List<String> values = filters.getValues();
- if (!values.contains(value)) {
- values.add(value);
- filters.setValues(values);
- filtersService.saveOrUpdate(filters);
- }
- } catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
- logger.error("Error invoking method on eventData",e);
- }
- }
- }
- }
-
- }
-
- /**
- * Handle as persistent event if marked persistent.
- *
- * @param event the event
- */
- private void handleAsPersistentEventIfMarkedPersistent(Event<AutomationEventImplementerI> event) {
- // Persist the event if this is a PersistentEventImplementerI
- if (event.getData() instanceof PersistentEventImplementerI) {
- try {
- final HibernatePersistentEventService service = XDAT.getContextService().getBean(HibernatePersistentEventService.class);
- service.create((PersistentEvent)event.getData());
- } catch (SecurityException | IllegalArgumentException e) {
- logger.error("Exception persisting event",e);
- }
- }
- }
-
- /**
- * Handle event.
- *
- * @param event the event
- */
- /* (non-Javadoc)
+ final AutomationEventImplementerI eventData = event.getData();
+ if (eventData.getEventId() == null || eventData.getClass() == null) {
+ return;
+ }
+ final List<AutomationEventIds> autoIds = _idsService.getEventIds(eventData.getExternalId(), eventData.getSrcEventClass(), true);
+ if (autoIds.size() < 1) {
+ final AutomationEventIds ids = new AutomationEventIds(eventData);
+ _idsService.saveOrUpdate(ids);
+ } else {
+ for (final AutomationEventIds ids : autoIds) {
+ if (!ids.getEventIds().contains(eventData.getEventId())) {
+ ids.getEventIds().add(eventData.getEventId());
+ _idsService.saveOrUpdate(ids);
+ }
+ }
+ }
+ final Class<? extends AutomationEventImplementerI> clazz = eventData.getClass();
+ for (final Method method : Arrays.asList(clazz.getMethods())) {
+ if (method.isAnnotationPresent(Filterable.class) && method.getName().substring(0, 3).equalsIgnoreCase("get")) {
+ final char c[] = method.getName().substring(3).toCharArray();
+ c[0] = Character.toLowerCase(c[0]);
+ final String column = new String(c);
+ AutomationFilters filters = _filtersService.getAutomationFilters(eventData.getExternalId(), eventData.getSrcEventClass(), column, true);
+ if (filters == null) {
+ filters = new AutomationFilters(eventData, column);
+ try {
+ _filtersService.saveOrUpdate(filters);
+ } catch (ConstraintViolationException e) {
+ logger.warn("A constraint violation error on {} occurred saving a filters entity: {}\n{}", e.getConstraintName(), filters.toString(), e.getMessage());
+ }
+ } else {
+ try {
+ final String value = method.invoke(eventData).toString();
+ final List<String> values = filters.getValues();
+ if (!values.contains(value)) {
+ values.add(value);
+ filters.setValues(values);
+ _filtersService.saveOrUpdate(filters);
+ }
+ } catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+ logger.error("Error invoking method on eventData", e);
+ }
+ }
+ }
+ }
+
+ }
+
+ /**
+ * Handle as persistent event if marked persistent.
+ *
+ * @param event the event
+ */
+ private void handleAsPersistentEventIfMarkedPersistent(Event<AutomationEventImplementerI> event) {
+ // Persist the event if this is a PersistentEventImplementerI
+ if (event.getData() instanceof PersistentEventImplementerI) {
+ try {
+ _persistentEventService.create((PersistentEvent) event.getData());
+ } catch (SecurityException | IllegalArgumentException e) {
+ logger.error("Exception persisting event", e);
+ }
+ }
+ }
+
+ /**
+ * Handle event.
+ *
+ * @param event the event
+ */
+ /* (non-Javadoc)
* @see org.nrg.xnat.event.listeners.WorkflowStatusEventHandlerAbst#handleEvent(org.nrg.xft.event.WorkflowStatusEvent)
*/
public void handleEvent(Event<AutomationEventImplementerI> event) {
- final AutomationEventImplementerI automationEvent = event.getData();
- if (automationEvent == null) {
- logger.debug("Automation script will not be launched because applicationEvent object is null");
- return;
- }
- final UserI user;
- try {
- user = Users.getUser(automationEvent.getUserId());
- } catch (UserNotFoundException | UserInitException e) {
- // User is required to launch script
- logger.debug("Automation not launching because user object is null");
- return;
- }
+ final AutomationEventImplementerI automationEvent = event.getData();
+ if (automationEvent == null) {
+ logger.debug("Automation script will not be launched because applicationEvent object is null");
+ return;
+ }
+ final UserI user;
+ try {
+ user = Users.getUser(automationEvent.getUserId());
+ } catch (UserNotFoundException | UserInitException e) {
+ // User is required to launch script
+ logger.debug("Automation not launching because user object is null");
+ return;
+ }
final String eventClass = automationEvent.getSrcEventClass();
if (eventClass == null) {
- logger.debug("Automation not launching because eventClass is null");
- return;
+ logger.debug("Automation not launching because eventClass is null");
+ return;
}
final String eventID = automationEvent.getEventId();
if (eventID == null) {
- logger.debug("Automation not launching because eventID is null");
- return;
+ logger.debug("Automation not launching because eventID is null");
+ return;
}
- final Map<String,String> filterMap = Maps.newHashMap();
- final Class<? extends AutomationEventImplementerI> clazz = automationEvent.getClass();
- for (final Method method : Arrays.asList(clazz.getMethods())) {
- if (method.isAnnotationPresent(Filterable.class) && method.getName().substring(0,3).equalsIgnoreCase("get")) {
- final char c[] = method.getName().substring(3).toCharArray();
- c[0] = Character.toLowerCase(c[0]);
- final String column = new String(c);
- String value;
- try {
- final Object rtValue = method.invoke(automationEvent);
- if (rtValue != null) {
- value = rtValue.toString();
- filterMap.put(column, value);
- }
- } catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
- logger.error("ERROR calling method on filterable field in event object", e);
- // Let's let this pass for now.
- }
- }
- }
- if (eventID == null) {
- logger.debug("Automation not launching because eventID is null");
- return;
+ final Map<String, String> filterMap = Maps.newHashMap();
+ final Class<? extends AutomationEventImplementerI> clazz = automationEvent.getClass();
+ for (final Method method : Arrays.asList(clazz.getMethods())) {
+ if (method.isAnnotationPresent(Filterable.class) && method.getName().substring(0, 3).equalsIgnoreCase("get")) {
+ final char c[] = method.getName().substring(3).toCharArray();
+ c[0] = Character.toLowerCase(c[0]);
+ final String column = new String(c);
+ String value;
+ try {
+ final Object rtValue = method.invoke(automationEvent);
+ if (rtValue != null) {
+ value = rtValue.toString();
+ filterMap.put(column, value);
+ }
+ } catch (IllegalAccessException | IllegalArgumentException | InvocationTargetException e) {
+ logger.error("ERROR calling method on filterable field in event object", e);
+ // Let's let this pass for now.
+ }
+ }
}
final String eventName = eventID.replaceAll("\\*OPEN\\*", "(").replaceAll("\\*CLOSE\\*", ")");
//check to see if this has been handled before
@@ -266,88 +293,90 @@ public class AutomationEventScriptHandler implements Consumer<Event<AutomationEv
for (final Script script : getScripts(automationEvent.getExternalId(), eventClass, eventID, filterMap)) {
try {
final String action = "Executed script " + script.getScriptId();
- Method justMethod = null;
- try {
- justMethod = automationEvent.getClass().getMethod("getJustification");
- } catch (NoSuchMethodException | NullPointerException | SecurityException e) {
- // Do nothing for now
- }
- final Object justObject = (justMethod!=null) ? justMethod.invoke(automationEvent) : null;
- final String justification = (justObject!=null) ? justObject.toString() : "";
+ Method justMethod = null;
+ try {
+ justMethod = automationEvent.getClass().getMethod("getJustification");
+ } catch (NoSuchMethodException | NullPointerException | SecurityException e) {
+ // Do nothing for now
+ }
+ final Object justObject = (justMethod != null) ? justMethod.invoke(automationEvent) : null;
+ final String justification = (justObject != null) ? justObject.toString() : "";
final String comment = "Executed script " + script.getScriptId() + " triggered by event " + eventID;
final PersistentWorkflowI scriptWrk = PersistentWorkflowUtils.buildOpenWorkflow(user, automationEvent.getEntityType(), automationEvent.getEntityId(), automationEvent.getExternalId(),
- EventUtils.newEventInstance(EventUtils.CATEGORY.DATA, EventUtils.TYPE.PROCESS, action,
- StringUtils.isNotBlank(justification) ? justification : "Automated execution: " + comment, comment));
+ EventUtils.newEventInstance(EventUtils.CATEGORY.DATA, EventUtils.TYPE.PROCESS, action,
+ StringUtils.isNotBlank(justification) ? justification : "Automated execution: " + comment, comment));
assert scriptWrk != null;
scriptWrk.setStatus(PersistentWorkflowUtils.QUEUED);
WorkflowUtils.save(scriptWrk, scriptWrk.buildEvent());
-
+
final AutomatedScriptRequest request = new AutomatedScriptRequest(automationEvent.getSrcStringifiedId(), automationEvent.getSrcEventClass(), user, script.getScriptId(), eventName,
- scriptWrk.getWorkflowId().toString(), automationEvent.getEntityType(), automationEvent.getSrcStringifiedId(), automationEvent.getExternalId(), automationEvent.getParameterMap());
-
+ scriptWrk.getWorkflowId().toString(), automationEvent.getEntityType(), automationEvent.getSrcStringifiedId(), automationEvent.getExternalId(), automationEvent.getParameterMap());
+
// We're running this here now, so we can return script output
//XDAT.sendJmsRequest(request);
final ScriptOutput scriptOut = executeScriptRequest(request);
if (automationCompletionEvent != null && scriptOut != null) {
- automationCompletionEvent.getScriptOutputs().add(scriptOut);
+ automationCompletionEvent.getScriptOutputs().add(scriptOut);
}
} catch (Exception e1) {
logger.error("Script launch exception", e1);
}
}
- if (automationCompletionEvent!= null && automationCompletionEvent.getScriptOutputs().size()>0) {
- XftEventService eventService = XftEventService.getService();
- if (eventService != null) {
- automationCompletionEvent.setEventCompletionTime(System.currentTimeMillis());
- eventService.triggerEvent(automationCompletionEvent);
- List<String> notifyList = automationCompletionEvent.getNotificationList();
- if (notifyList != null && !notifyList.isEmpty()) {
- AdminUtils.sendUserHTMLEmail(EMAIL_SUBJECT, scriptOutputToHtmlString(automationCompletionEvent.getScriptOutputs()), false, notifyList.toArray(new String[0]));
- }
- }
+ if (automationCompletionEvent != null && automationCompletionEvent.getScriptOutputs().size() > 0) {
+ XftEventService eventService = XftEventService.getService();
+ if (eventService != null) {
+ automationCompletionEvent.setEventCompletionTime(System.currentTimeMillis());
+ eventService.triggerEvent(automationCompletionEvent);
+ List<String> notifyList = automationCompletionEvent.getNotificationList();
+ if (notifyList != null && !notifyList.isEmpty()) {
+ final String EMAIL_SUBJECT = "Automation Results";
+ AdminUtils.sendUserHTMLEmail(EMAIL_SUBJECT, scriptOutputToHtmlString(automationCompletionEvent.getScriptOutputs()), false, notifyList.toArray(new String[0]));
+ }
+ }
+ }
+ }
+
+ private String scriptOutputToHtmlString(List<ScriptOutput> scriptOutputs) {
+ if (scriptOutputs == null) {
+ return "";
+ }
+ StringBuilder sb = new StringBuilder();
+ for (ScriptOutput scriptOut : scriptOutputs) {
+ sb.append("<br><b>SCRIPT EXECUTION RESULTS</b><br>");
+ sb.append("<br><b>FINAL STATUS: ").append(scriptOut.getStatus()).append("</b><br>");
+ if (scriptOut.getStatus().equals(Status.ERROR) && scriptOut.getResults() != null && scriptOut.getResults().toString().length() > 0) {
+ sb.append("<br><b>SCRIPT RESULTS</b><br>");
+ sb.append(scriptOut.getResults().toString().replace("\n", "<br>"));
+ }
+ if (scriptOut.getOutput() != null && scriptOut.getOutput().length() > 0) {
+ sb.append("<br><b>SCRIPT STDOUT</b><br>");
+ sb.append(scriptOut.getOutput().replace("\n", "<br>"));
+ }
+ if (scriptOut.getErrorOutput() != null && scriptOut.getErrorOutput().length() > 0) {
+ sb.append("<br><b>SCRIPT STDERR/EXCEPTION</b><br>");
+ sb.append(scriptOut.getErrorOutput().replace("\n", "<br>"));
+ }
}
+ return sb.toString();
}
- private String scriptOutputToHtmlString(List<ScriptOutput> scriptOutputs) {
- if (scriptOutputs == null) {
- return "";
- }
- StringBuilder sb = new StringBuilder();
- for (ScriptOutput scriptOut : scriptOutputs) {
- sb.append("<br><b>SCRIPT EXECUTION RESULTS</b><br>");
- sb.append("<br><b>FINAL STATUS: " + scriptOut.getStatus() + "</b><br>");
- if (scriptOut.getStatus().equals(Status.ERROR) && scriptOut.getResults()!=null && scriptOut.getResults().toString().length()>0) {
- sb.append("<br><b>SCRIPT RESULTS</b><br>");
- sb.append(scriptOut.getResults().toString().replace("\n", "<br>"));
- }
- if (scriptOut.getOutput()!=null && scriptOut.getOutput().length()>0) {
- sb.append("<br><b>SCRIPT STDOUT</b><br>");
- sb.append(scriptOut.getOutput().replace("\n", "<br>"));
- }
- if (scriptOut.getErrorOutput()!=null && scriptOut.getErrorOutput().length()>0) {
- sb.append("<br><b>SCRIPT STDERR/EXCEPTION</b><br>");
- sb.append(scriptOut.getErrorOutput().replace("\n", "<br>"));
- }
- }
- return sb.toString();
- }
-
- /**
+ /**
* Gets the scripts.
*
- * @param projectId the project id
+ * @param projectId the project id
* @param eventClass the event class
- * @param event the event
- * @param filterMap the filter map
+ * @param event the event
+ * @param filterMap the filter map
+ *
* @return the scripts
*/
- private List<Script> getScripts(final String projectId, String eventClass, String event, Map<String,String> filterMap) {
+ private List<Script> getScripts(final String projectId, String eventClass, String event, Map<String, String> filterMap) {
final List<Script> scripts = Lists.newArrayList();
//project level scripts
if (StringUtils.isNotBlank(projectId)) {
-
+
final Script script = _service.getScript(Scope.Project, projectId, eventClass, event, filterMap);
if (script != null) {
scripts.add(script);
@@ -362,17 +391,23 @@ public class AutomationEventScriptHandler implements Consumer<Event<AutomationEv
return scripts;
}
-
+
/**
* Execute script request.
*
* @param request the request
+ *
* @return the script output
+ *
* @throws Exception the exception
*/
private ScriptOutput executeScriptRequest(AutomatedScriptRequest request) throws Exception {
-
final PersistentWorkflowI workflow = WorkflowUtils.getUniqueWorkflow(request.getUser(), request.getScriptWorkflowId());
+ if (workflow == null) {
+ logger.warn("Didn't find the workflow indicated by an automated script request: " + request.getScriptWorkflowId() + " (requested by " + request.getUser().getUsername() + ")");
+ return null;
+ }
+
workflow.setStatus(PersistentWorkflowUtils.IN_PROGRESS);
WorkflowUtils.save(workflow, workflow.buildEvent());
@@ -388,8 +423,8 @@ public class AutomationEventScriptHandler implements Consumer<Event<AutomationEv
parameters.put("dataId", request.getDataId());
parameters.put("externalId", request.getExternalId());
parameters.put("workflow", workflow);
- if (request.getArgumentMap()!=null && !request.getArgumentMap().isEmpty()) {
- parameters.putAll(request.getArgumentMap());
+ if (request.getArgumentMap() != null && !request.getArgumentMap().isEmpty()) {
+ parameters.putAll(request.getArgumentMap());
}
ScriptOutput scriptOut = null;
@@ -400,12 +435,12 @@ public class AutomationEventScriptHandler implements Consumer<Event<AutomationEv
}
} catch (NrgServiceException e) {
final String message = String.format("Failed running the script %s by user %s for event %s on data type %s instance %s from project %s",
- request.getScriptId(),
- request.getUser().getLogin(),
- request.getEvent(),
- request.getDataType(),
- request.getDataId(),
- request.getExternalId());
+ request.getScriptId(),
+ request.getUser().getLogin(),
+ request.getEvent(),
+ request.getDataType(),
+ request.getDataId(),
+ request.getExternalId());
AdminUtils.sendAdminEmail("Script execution failure", message);
logger.error(message, e);
if (PersistentWorkflowUtils.IN_PROGRESS.equals(workflow.getStatus())) {
@@ -413,6 +448,5 @@ public class AutomationEventScriptHandler implements Consumer<Event<AutomationEv
}
}
return scriptOut;
- }
-
+ }
}
diff --git a/src/main/java/org/nrg/xnat/configuration/DatabaseConfig.java b/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
similarity index 60%
rename from src/main/java/org/nrg/xnat/configuration/DatabaseConfig.java
rename to src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
index b8da1456..60a1063b 100644
--- a/src/main/java/org/nrg/xnat/configuration/DatabaseConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
@@ -1,40 +1,26 @@
-package org.nrg.xnat.configuration;
+package org.nrg.xnat.initialization;
-import org.hibernate.cache.ehcache.SingletonEhCacheRegionFactory;
-import org.hibernate.cache.spi.RegionFactory;
-import org.hibernate.cfg.ImprovedNamingStrategy;
import org.nrg.framework.exceptions.NrgServiceError;
import org.nrg.framework.exceptions.NrgServiceException;
-import org.nrg.framework.orm.hibernate.AggregatedAnnotationSessionFactoryBean;
-import org.nrg.framework.orm.hibernate.HibernateEntityPackageList;
-import org.nrg.framework.orm.hibernate.PrefixedTableNamingStrategy;
import org.nrg.framework.utilities.Beans;
import org.postgresql.Driver;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import org.springframework.beans.factory.config.PropertiesFactoryBean;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.Configuration;
import org.springframework.core.env.Environment;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jdbc.datasource.SimpleDriverDataSource;
-import org.springframework.orm.hibernate4.HibernateTransactionManager;
-import org.springframework.orm.hibernate4.LocalSessionFactoryBean;
-import org.springframework.transaction.PlatformTransactionManager;
-import org.springframework.transaction.annotation.EnableTransactionManagement;
import javax.inject.Inject;
import javax.sql.DataSource;
-import java.io.IOException;
import java.lang.reflect.InvocationTargetException;
-import java.util.List;
import java.util.Properties;
/**
* Sets up the database configuration for XNAT.
*/
@Configuration
-@EnableTransactionManagement(proxyTargetClass = true)
public class DatabaseConfig {
public static final String DEFAULT_DATASOURCE_URL = "jdbc:postgresql://localhost/xnat";
@@ -71,51 +57,6 @@ public class DatabaseConfig {
return new JdbcTemplate(dataSource());
}
- @Bean
- public ImprovedNamingStrategy namingStrategy() {
- return new PrefixedTableNamingStrategy("xhbm");
- }
-
- @Bean
- public PropertiesFactoryBean hibernateProperties() {
- final PropertiesFactoryBean bean = new PropertiesFactoryBean();
- final Properties properties = Beans.getNamespacedProperties(_environment, "hibernate", false);
- if (properties.size() == 0) {
- properties.putAll(DEFAULT_HIBERNATE_PROPERTIES);
- }
- bean.setProperties(properties);
- return bean;
- }
-
- @Bean
- public RegionFactory regionFactory() throws NrgServiceException {
- try {
- return new SingletonEhCacheRegionFactory(hibernateProperties().getObject());
- } catch (IOException e) {
- throw new NrgServiceException(NrgServiceError.Unknown, "An error occurred trying to retrieve the Hibernate properties", e);
- }
- }
-
- @Bean
- public LocalSessionFactoryBean sessionFactory(final List<HibernateEntityPackageList> packageLists) throws NrgServiceException {
- try {
- final AggregatedAnnotationSessionFactoryBean bean = new AggregatedAnnotationSessionFactoryBean();
- bean.setEntityPackageLists(packageLists);
- bean.setDataSource(dataSource());
- bean.setCacheRegionFactory(regionFactory());
- bean.setHibernateProperties(hibernateProperties().getObject());
- bean.setNamingStrategy(namingStrategy());
- return bean;
- } catch (IOException e) {
- throw new NrgServiceException(NrgServiceError.Unknown, "An error occurred trying to retrieve the Hibernate properties", e);
- }
- }
-
- @Bean
- public PlatformTransactionManager transactionManager(final List<HibernateEntityPackageList> packageLists) throws NrgServiceException {
- return new HibernateTransactionManager(sessionFactory(packageLists).getObject());
- }
-
private static Properties setDefaultDatasourceProperties(final Properties properties) {
// Configure some defaults if they're not already set.
if (!properties.containsKey("class")) {
@@ -153,14 +94,6 @@ public class DatabaseConfig {
private static final Logger _log = LoggerFactory.getLogger(DatabaseConfig.class);
- private static final Properties DEFAULT_HIBERNATE_PROPERTIES = new Properties() {{
- setProperty("hibernate.dialect", "org.hibernate.dialect.PostgreSQL9Dialect");
- setProperty("hibernate.hbm2ddl.auto", "update");
- setProperty("hibernate.show_sql", "false");
- setProperty("hibernate.cache.use_second_level_cache", "true");
- setProperty("hibernate.cache.use_query_cache", "true");
- }};
-
@Inject
private Environment _environment;
}
diff --git a/src/main/java/org/nrg/xnat/initialization/InitializerSiteConfiguration.java b/src/main/java/org/nrg/xnat/initialization/InitializerSiteConfiguration.java
deleted file mode 100644
index f5714bba..00000000
--- a/src/main/java/org/nrg/xnat/initialization/InitializerSiteConfiguration.java
+++ /dev/null
@@ -1,154 +0,0 @@
-/**
- * InitializerSiteConfig
- * (C) 2016 Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD License
- */
-package org.nrg.xnat.initialization;
-
-import org.apache.commons.lang3.StringUtils;
-import org.nrg.config.exceptions.SiteConfigurationException;
-import org.nrg.config.services.impl.PropertiesBasedSiteConfigurationService;
-import org.nrg.framework.exceptions.NrgServiceError;
-import org.nrg.framework.exceptions.NrgServiceRuntimeException;
-import org.nrg.framework.services.SerializerService;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.dao.DataAccessException;
-import org.springframework.jdbc.core.ResultSetExtractor;
-import org.springframework.stereotype.Service;
-
-import javax.inject.Inject;
-import java.io.IOException;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.Map;
-import java.util.Properties;
-
-@Service
-public class InitializerSiteConfiguration extends PropertiesBasedSiteConfigurationService {
- public String getSiteConfigurationService() throws SiteConfigurationException {
- return getSiteConfigurationProperty("admin.siteConfig.service");
- }
-
- public String getPasswordComplexity() throws SiteConfigurationException {
- return getSiteConfigurationProperty("passwordComplexity");
- }
-
- public String getPasswordComplexityMessage() throws SiteConfigurationException {
- return getSiteConfigurationProperty("passwordComplexityMessage");
- }
-
- public int getPasswordHistoryDuration() throws SiteConfigurationException {
- return getIntegerSiteConfigurationProperty("passwordHistoryDuration");
- }
-
- public String getReceivedFileUser() throws SiteConfigurationException {
- return getSiteConfigurationProperty("receivedFileUser");
- }
-
- public int getInactivityBeforeLockout() throws SiteConfigurationException {
- return getIntegerSiteConfigurationProperty("inactivityBeforeLockout");
- }
-
- public long getInactivityBeforeLockoutSchedule() throws SiteConfigurationException {
- return getLongSiteConfigurationProperty("inactivityBeforeLockoutSchedule");
- }
-
- public long getMaxFailedLoginsLockoutDuration() throws SiteConfigurationException {
- return getLongSiteConfigurationProperty("maxFailedLoginsLockoutDuration");
- }
-
- public double getSessionXmlRebuilderInterval() throws SiteConfigurationException {
- return getDoubleSiteConfigurationProperty("sessionXmlRebuilderInterval");
- }
-
- public long getSessionXmlRebuilderRepeat() throws SiteConfigurationException {
- return getLongSiteConfigurationProperty("sessionXmlRebuilderRepeat");
- }
-
- public String getAliasTokenTimeout() throws SiteConfigurationException {
- return getSiteConfigurationProperty("aliasTokenTimeout");
- }
-
- public Map<String, String> getSmtpServer() throws SiteConfigurationException, IOException {
- final String definition = getSiteConfigurationProperty("smtpServer");
- if (StringUtils.isBlank(definition)) {
- return null;
- }
- return _serializerService.deserializeJsonToMapOfStrings(definition);
- }
-
- public String getAdminEmail() throws SiteConfigurationException {
- return getSiteConfigurationProperty("adminEmail");
- }
-
- public String getEmailPrefix() throws SiteConfigurationException {
- return getSiteConfigurationProperty("emailPrefix");
- }
-
- public String getFeatureService() throws SiteConfigurationException {
- return getSiteConfigurationProperty("featureService");
- }
-
- public String getFeatureRepositoryService() throws SiteConfigurationException {
- return getSiteConfigurationProperty("featureRepositoryService");
- }
-
- public String getRoleService() throws SiteConfigurationException {
- return getSiteConfigurationProperty("roleService");
- }
-
- public String getRoleRepositoryService() throws SiteConfigurationException {
- return getSiteConfigurationProperty("roleRepositoryService");
- }
-
- @Override
- protected void setPreferenceValue(final String username, final String property, final String value) {
- throw new NrgServiceRuntimeException(NrgServiceError.PermissionsViolation, "This site configuration service is for initialization and is read only.");
- }
-
- @Override
- protected void getPreferenceValuesFromPersistentStore(final Properties properties) {
- final Integer siteConfigToolKey = getSiteConfigToolKey();
- if (siteConfigToolKey == null) {
- _log.info("Didn't find a tool for the {} ID, checking for import values from configuration service.", SITE_CONFIG_TOOL_ID);
- final Properties existing = checkForConfigServiceSiteConfiguration();
- if (existing != null) {
- _log.info("Found {} properties in the configuration service, importing those.", existing.size());
- properties.putAll(existing);
- }
- } else {
- _log.info("Working with the existing {} tool, checking for new import values.", SITE_CONFIG_TOOL_ID);
- properties.putAll(getPersistedSiteConfiguration(siteConfigToolKey));
- }
- }
-
- @SuppressWarnings({"SqlDialectInspection", "SqlNoDataSourceInspection"})
- private Properties getPersistedSiteConfiguration(final int toolId) {
- return getJdbcTemplate().query("select name, value from xhbm_preference where tool = ?", PROPERTIES_RESULT_SET_EXTRACTOR, toolId);
- }
-
- @SuppressWarnings({"SqlDialectInspection", "SqlNoDataSourceInspection"})
- private Integer getSiteConfigToolKey() {
- return getJdbcTemplate().queryForObject("select id from xhbm_tool where tool_id = ?", Integer.class, SITE_CONFIG_TOOL_ID);
- }
-
- private static final ResultSetExtractor<Properties> PROPERTIES_RESULT_SET_EXTRACTOR = new ResultSetExtractor<Properties>() {
- @Override
- public Properties extractData(final ResultSet results) throws SQLException, DataAccessException {
- final Properties properties = new Properties();
- while (results.next()) {
- properties.put(results.getString("name"), results.getString("value"));
- }
- return properties;
- }
- };
-
- private static final Logger _log = LoggerFactory.getLogger(InitializerSiteConfiguration.class);
- private static final String SITE_CONFIG_TOOL_ID = "siteConfig";
-
- @Inject
- private SerializerService _serializerService;
-}
diff --git a/src/main/java/org/nrg/xnat/initialization/InitializingTask.java b/src/main/java/org/nrg/xnat/initialization/InitializingTask.java
new file mode 100644
index 00000000..9fc1ed68
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/InitializingTask.java
@@ -0,0 +1,15 @@
+package org.nrg.xnat.initialization;
+
+import java.util.Date;
+
+public interface InitializingTask extends Runnable {
+ String getTaskName();
+
+ boolean isCompleted();
+
+ Date completedAt();
+
+ void complete();
+
+ void reset();
+}
diff --git a/src/main/java/org/nrg/xnat/initialization/InitializingTasksExecutor.java b/src/main/java/org/nrg/xnat/initialization/InitializingTasksExecutor.java
new file mode 100644
index 00000000..64fbd2d1
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/InitializingTasksExecutor.java
@@ -0,0 +1,38 @@
+package org.nrg.xnat.initialization;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.context.event.ContextRefreshedEvent;
+import org.springframework.context.event.EventListener;
+import org.springframework.stereotype.Component;
+
+import java.util.List;
+
+@Component
+public class InitializingTasksExecutor {
+ @EventListener
+ public void executeOnContextRefresh(final ContextRefreshedEvent event) {
+ if (_log.isDebugEnabled()) {
+ _log.debug("Handling context refreshed event at " + event.getTimestamp());
+ }
+ for (final InitializingTask task : _tasks) {
+ if (!task.isCompleted()) {
+ if (_log.isInfoEnabled()) {
+ _log.info("Executing type: " + task.getTaskName());
+ }
+ task.run();
+ if (_log.isInfoEnabled()) {
+ _log.info("Task \"" + task.getTaskName() + "\" " + (task.isCompleted() ? "completed at " + task.completedAt() : "did not complete."));
+ }
+ }
+ }
+ }
+
+ private static final Logger _log = LoggerFactory.getLogger(InitializingTasksExecutor.class);
+
+ @Autowired
+ @Lazy
+ private List<InitializingTask> _tasks;
+}
diff --git a/src/main/java/org/nrg/xnat/configuration/PropertiesConfig.java b/src/main/java/org/nrg/xnat/initialization/PropertiesConfig.java
similarity index 99%
rename from src/main/java/org/nrg/xnat/configuration/PropertiesConfig.java
rename to src/main/java/org/nrg/xnat/initialization/PropertiesConfig.java
index 124bd166..af431c4d 100644
--- a/src/main/java/org/nrg/xnat/configuration/PropertiesConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/PropertiesConfig.java
@@ -1,4 +1,4 @@
-package org.nrg.xnat.configuration;
+package org.nrg.xnat.initialization;
import org.apache.commons.configuration.ConfigurationException;
import org.apache.commons.lang3.StringUtils;
diff --git a/src/main/java/org/nrg/xnat/initialization/RootConfig.java b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
index 963fdb5f..cd76f5bf 100644
--- a/src/main/java/org/nrg/xnat/initialization/RootConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
@@ -1,99 +1,83 @@
package org.nrg.xnat.initialization;
-import org.nrg.config.exceptions.SiteConfigurationException;
-import org.nrg.framework.configuration.FrameworkConfig;
+import com.fasterxml.jackson.core.JsonParser;
+import com.fasterxml.jackson.core.PrettyPrinter;
+import com.fasterxml.jackson.core.util.DefaultIndenter;
+import com.fasterxml.jackson.core.util.DefaultPrettyPrinter;
+import com.fasterxml.jackson.databind.ObjectMapper;
+import com.fasterxml.jackson.dataformat.yaml.YAMLFactory;
import org.nrg.framework.datacache.SerializerRegistry;
-import org.nrg.framework.orm.hibernate.HibernateEntityPackageList;
+import org.nrg.framework.exceptions.NrgServiceException;
import org.nrg.framework.services.ContextService;
-import org.nrg.xdat.security.HistoricPasswordValidator;
-import org.nrg.xdat.security.PasswordValidatorChain;
-import org.nrg.xdat.security.RegExpValidator;
-import org.nrg.xnat.event.conf.EventPackages;
-import org.nrg.xnat.restlet.XnatRestletExtensions;
-import org.nrg.xnat.restlet.actions.importer.ImporterHandlerPackages;
-import org.nrg.xnat.utils.XnatUserProvider;
-import org.springframework.context.annotation.*;
-
-import javax.inject.Inject;
-import java.util.Arrays;
-import java.util.Collections;
-import java.util.HashSet;
-import java.util.List;
-
+import org.nrg.framework.services.SerializerService;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
+import org.nrg.xnat.helpers.prearchive.PrearcConfig;
+import org.springframework.context.annotation.Bean;
+import org.springframework.context.annotation.Configuration;
+import org.springframework.context.annotation.Import;
+import org.springframework.context.annotation.ImportResource;
+
+/**
+ * Configuration for the XNAT root application context. This contains all of the basic infrastructure for initializing
+ * and bootstrapping the site, including data source configuration, transaction and session management, and site
+ * configuration preferences.
+ *
+ * <b>NOTE:</b> If you are adding code to this class, please be sure you know what you're doing! Most configuration code
+ * for standard XNAT components should be added in {@link org.nrg.xnat.configuration.ApplicationConfig}
+ */
@Configuration
-@ComponentScan({"org.nrg.xdat.daos", "org.nrg.xnat.daos", "org.nrg.xnat.services.impl.hibernate", "org.nrg.xdat.services", "org.nrg.xft.daos", "org.nrg.xft.services", "org.nrg.xnat.helpers.merge", "org.nrg.xnat.configuration", "org.nrg.xnat.services", "org.nrg.dicomtools.filters"})
-@Import(FrameworkConfig.class)
-@ImportResource({"WEB-INF/conf/xnat-security.xml", "WEB-INF/conf/mq-context.xml"})
+@Import({PropertiesConfig.class, DatabaseConfig.class})
+@ImportResource("WEB-INF/conf/xnat-security.xml")
public class RootConfig {
-
- public static final List<String> DEFAULT_ENTITY_PACKAGES = Arrays.asList("org.nrg.xft.entities", "org.nrg.xft.event.entities", "org.nrg.xdat.entities", "org.nrg.xnat.entities", "org.nrg.xnat.event.entities", "org.nrg.config.entities");
-
@Bean
public InitializerSiteConfiguration initializerSiteConfiguration() {
return new InitializerSiteConfiguration();
}
@Bean
- public RegExpValidator regexValidator() throws SiteConfigurationException {
- final String complexityExpression = _preferences.getPasswordComplexity();
- final String complexityMessage = _preferences.getPasswordComplexityMessage();
- return new RegExpValidator(complexityExpression, complexityMessage);
- }
-
- @Bean
- public HistoricPasswordValidator historicPasswordValidator() throws SiteConfigurationException {
- final int durationInDays = _preferences.getPasswordHistoryDuration();
- return new HistoricPasswordValidator(durationInDays);
- }
-
- @Bean
- public PasswordValidatorChain validator(final RegExpValidator regExpValidator, final HistoricPasswordValidator historicPasswordValidator) {
- return new PasswordValidatorChain(Arrays.asList(regExpValidator, historicPasswordValidator));
- }
-
- // MIGRATION: I'm not even sure this is used, but we need to do away with it in favor of prefs.
- @Bean
- public List<String> propertiesRepositories() {
- return Collections.singletonList("WEB-INF/conf/properties");
- }
-
- @Bean
- public ContextService contextService() {
+ public ContextService rootContextService() throws NrgServiceException {
return ContextService.getInstance();
}
@Bean
- public HibernateEntityPackageList coreXnatEntityPackages() {
- return new HibernateEntityPackageList(DEFAULT_ENTITY_PACKAGES);
+ public PrearcConfig prearcConfig() {
+ final PrearcConfig prearcConfig = new PrearcConfig();
+ prearcConfig.setReloadPrearcDatabaseOnApplicationStartup(false);
+ return prearcConfig;
}
@Bean
- public XnatUserProvider receivedFileUserProvider() throws SiteConfigurationException {
- final String receivedFileUser = _preferences.getReceivedFileUser();
- return new XnatUserProvider(receivedFileUser);
+ public PrettyPrinter prettyPrinter() {
+ final DefaultIndenter indenter = new DefaultIndenter(" ", DefaultIndenter.SYS_LF);
+ return new DefaultPrettyPrinter() {{
+ indentObjectsWith(indenter);
+ indentArraysWith(indenter);
+ }};
}
@Bean
- public XnatRestletExtensions xnatRestletExtensions() {
- return new XnatRestletExtensions(new HashSet<>(Arrays.asList(new String[]{"org.nrg.xnat.restlet.extensions"})));
+ public ObjectMapper jsonObjectMapper() {
+ final PrettyPrinter printer = prettyPrinter();
+ final ObjectMapper mapper = new ObjectMapper().setDefaultPrettyPrinter(printer);
+ mapper.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
+ return mapper;
}
@Bean
- public ImporterHandlerPackages importerHandlerPackages() {
- return new ImporterHandlerPackages(new HashSet<>(Arrays.asList(new String[]{"org.nrg.xnat.restlet.actions", "org.nrg.xnat.archive"})));
+ public ObjectMapper yamlObjectMapper() {
+ final PrettyPrinter printer = prettyPrinter();
+ final ObjectMapper mapper = new ObjectMapper(new YAMLFactory()).setDefaultPrettyPrinter(printer);
+ mapper.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
+ return mapper;
}
@Bean
- public EventPackages eventPackages() {
- // NOTE: These should be treated as parent packages. All sub-packages should be searched
- return new EventPackages(new HashSet<>(Arrays.asList(new String[]{"org.nrg.xnat.event", "org.nrg.xft.event", "org.nrg.xdat.event"})));
+ public SerializerService serializerService() {
+ return new SerializerService();
}
@Bean
public SerializerRegistry serializerRegistry() {
return new SerializerRegistry();
}
-
- @Inject
- private InitializerSiteConfiguration _preferences;
}
diff --git a/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java b/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
index 3c4f7fcd..20466e40 100644
--- a/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
+++ b/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
@@ -10,6 +10,7 @@ import org.nrg.framework.processors.XnatPluginBean;
import org.nrg.framework.utilities.BasicXnatResourceLocator;
import org.nrg.xdat.servlet.XDATAjaxServlet;
import org.nrg.xdat.servlet.XDATServlet;
+import org.nrg.xnat.configuration.ApplicationConfig;
import org.nrg.xnat.restlet.servlet.XNATRestletServlet;
import org.nrg.xnat.restlet.util.UpdateExpirationCookie;
import org.nrg.xnat.security.XnatSessionEventPublisher;
@@ -17,6 +18,7 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.core.io.Resource;
import org.springframework.core.io.support.PropertiesLoaderUtils;
+import org.springframework.stereotype.Service;
import org.springframework.web.filter.DelegatingFilterProxy;
import org.springframework.web.servlet.support.AbstractAnnotationConfigDispatcherServletInitializer;
@@ -62,20 +64,20 @@ public class XnatWebAppInitializer extends AbstractAnnotationConfigDispatcherSer
@Override
protected String[] getServletMappings() {
- return new String[] {"/admin/*", "/xapi/*"};
+ return new String[]{"/admin/*", "/xapi/*"};
}
@Override
protected Class<?>[] getRootConfigClasses() {
- final List<Class<?>> configClasses = new ArrayList<>();
- configClasses.add(RootConfig.class);
- configClasses.addAll(getPluginConfigs());
- return configClasses.toArray(new Class[configClasses.size()]);
+ return new Class<?>[]{RootConfig.class};
}
@Override
protected Class<?>[] getServletConfigClasses() {
- return new Class<?>[0];
+ final List<Class<?>> configClasses = new ArrayList<>();
+ configClasses.add(ApplicationConfig.class);
+ configClasses.addAll(getPluginConfigs());
+ return configClasses.toArray(new Class[configClasses.size()]);
}
@Override
@@ -115,9 +117,9 @@ public class XnatWebAppInitializer extends AbstractAnnotationConfigDispatcherSer
final List<Class<?>> configs = new ArrayList<>();
try {
for (final Resource resource : BasicXnatResourceLocator.getResources("classpath*:META-INF/xnat/**/*-plugin.properties")) {
- final Properties properties = PropertiesLoaderUtils.loadProperties(resource);
- final XnatPluginBean plugin = new XnatPluginBean(properties);
- final Class<?> config = plugin.getConfigClass();
+ final Properties properties = PropertiesLoaderUtils.loadProperties(resource);
+ final XnatPluginBean plugin = new XnatPluginBean(properties);
+ final Class<?> config = plugin.getConfigClass();
configs.add(config);
}
} catch (IOException e) {
@@ -130,7 +132,7 @@ public class XnatWebAppInitializer extends AbstractAnnotationConfigDispatcherSer
}
private void addServlet(final Class<? extends Servlet> clazz, final int loadOnStartup, final String... mappings) {
- final String name = StringUtils.uncapitalize(clazz.getSimpleName());
+ final String name = StringUtils.uncapitalize(clazz.getSimpleName());
final ServletRegistration.Dynamic registration = _context.addServlet(name, clazz);
registration.setLoadOnStartup(loadOnStartup);
registration.addMapping(mappings);
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/AbstractInitializingTask.java b/src/main/java/org/nrg/xnat/initialization/tasks/AbstractInitializingTask.java
new file mode 100644
index 00000000..20681767
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/AbstractInitializingTask.java
@@ -0,0 +1,35 @@
+package org.nrg.xnat.initialization.tasks;
+
+import org.nrg.xnat.initialization.InitializingTask;
+
+import java.util.Date;
+
+public abstract class AbstractInitializingTask implements InitializingTask {
+ @Override
+ public abstract String getTaskName();
+
+ @Override
+ public abstract void run();
+
+ @Override
+ public boolean isCompleted() {
+ return _completedAt != null;
+ }
+
+ @Override
+ public Date completedAt() {
+ return _completedAt;
+ }
+
+ @Override
+ public void complete() {
+ _completedAt = new Date();
+ }
+
+ @Override
+ public void reset() {
+ _completedAt = null;
+ }
+
+ private Date _completedAt;
+}
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/EncryptXnatPasswords.java b/src/main/java/org/nrg/xnat/initialization/tasks/EncryptXnatPasswords.java
new file mode 100644
index 00000000..e6968b17
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/EncryptXnatPasswords.java
@@ -0,0 +1,86 @@
+/*
+ * org.nrg.xnat.initialization.tasks.XnatPasswordEncrypter
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2016, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ */
+package org.nrg.xnat.initialization.tasks;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.dao.DataAccessException;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.ResultSetExtractor;
+import org.springframework.security.authentication.encoding.ShaPasswordEncoder;
+import org.springframework.stereotype.Component;
+
+import java.sql.Connection;
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.HashMap;
+import java.util.Map;
+
+@Component
+public class EncryptXnatPasswords extends AbstractInitializingTask {
+ @Override
+ public String getTaskName() {
+ return "Encrypt XNAT passwords";
+ }
+
+ @Override
+ public void run() {
+ try {
+ final PasswordResultSetExtractor extractor = new PasswordResultSetExtractor();
+ final Map<Integer, String> userPasswords = _template.query("SELECT xdat_user_id, primary_password FROM xdat_user WHERE primary_password IS NOT NULL AND length(primary_password) != 64", extractor);
+ final Map<Integer, String> historyPasswords = _template.query("SELECT history_id, primary_password FROM xdat_user_history WHERE primary_password IS NOT NULL AND length(primary_password) != 64", extractor);
+
+ for (final int userId : userPasswords.keySet()) {
+ _template.update("UPDATE xdat_user SET primary_password = ? WHERE xdat_user_id = ?", userPasswords.get(userId), userId);
+ }
+
+ for (int historyId : historyPasswords.keySet()) {
+ _template.update("UPDATE xdat_user_history SET primary_password = ? WHERE history_id = ?", userPasswords.get(historyId), historyId);
+ }
+
+ if ((!userPasswords.isEmpty() || !historyPasswords.isEmpty()) && tableExists("xs_item_cache")) {
+ _template.update("DELETE FROM xs_item_cache");
+ }
+
+ complete();
+ } catch (Exception e) {
+ logger.error("", e);
+ }
+ }
+
+ private boolean tableExists(final String name) throws SQLException {
+ try (final Connection connection = _template.getDataSource().getConnection();
+ final ResultSet results = connection.getMetaData().getTables("catalog", null, name, new String[]{"table"})) {
+ if (results.next()) {
+ return true;
+ }
+ }
+ return false;
+ }
+
+ private static class PasswordResultSetExtractor implements ResultSetExtractor<Map<Integer, String>> {
+ @Override
+ public Map<Integer, String> extractData(final ResultSet results) throws SQLException, DataAccessException {
+ final Map<Integer, String> passwords = new HashMap<>();
+ while (results.next()) {
+ passwords.put(results.getInt(1), encoder.encodePassword(results.getString(2), null));
+ }
+ return passwords;
+ }
+ final ShaPasswordEncoder encoder = new ShaPasswordEncoder(256);
+ }
+
+ private static Logger logger = LoggerFactory.getLogger(EncryptXnatPasswords.class);
+
+ @Autowired
+ @Lazy
+ private JdbcTemplate _template;
+}
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/GetSiteWideAnonScript.java b/src/main/java/org/nrg/xnat/initialization/tasks/GetSiteWideAnonScript.java
new file mode 100644
index 00000000..eae59e03
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/GetSiteWideAnonScript.java
@@ -0,0 +1,48 @@
+package org.nrg.xnat.initialization.tasks;
+
+import org.apache.commons.io.FileUtils;
+import org.nrg.config.entities.Configuration;
+import org.nrg.xdat.preferences.SiteConfigPreferences;
+import org.nrg.xnat.helpers.editscript.DicomEdit;
+import org.nrg.xnat.helpers.merge.AnonUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.stereotype.Component;
+
+@Component
+public class GetSiteWideAnonScript extends AbstractInitializingTask {
+ @Override
+ public String getTaskName() {
+ return "Get site-wide anon script";
+ }
+
+ @Override
+ public void run() {
+ try {
+ final String path = DicomEdit.buildScriptPath(DicomEdit.ResourceScope.SITE_WIDE, "");
+ final Configuration initConfig = AnonUtils.getService().getScript(path, null);
+ if (initConfig == null) {
+ _log.info("Creating Script Table.");
+ final String siteWideScript = FileUtils.readFileToString(AnonUtils.getDefaultScript());
+ final String adminUser = _preferences.getReceivedFileUser();
+ if (adminUser != null) {
+ AnonUtils.getService().setSiteWideScript(adminUser, path, siteWideScript);
+ } else {
+ throw new Exception("Site administrator not found.");
+ }
+ }
+ // there is a default site-wide script, so nothing to do here for the else.
+ complete();
+ } catch (Throwable e) {
+ _log.error("Unable to either find or initialize script database", e);
+ }
+ }
+
+ private static final Logger _log = LoggerFactory.getLogger(GetSiteWideAnonScript.class);
+
+ @Autowired
+ @Lazy
+ private SiteConfigPreferences _preferences;
+}
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/GetSiteWidePETTracerList.java b/src/main/java/org/nrg/xnat/initialization/tasks/GetSiteWidePETTracerList.java
new file mode 100644
index 00000000..4942dae0
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/GetSiteWidePETTracerList.java
@@ -0,0 +1,53 @@
+package org.nrg.xnat.initialization.tasks;
+
+import org.apache.commons.io.FileUtils;
+import org.nrg.config.entities.Configuration;
+import org.nrg.xdat.security.helpers.Roles;
+import org.nrg.xdat.security.helpers.Users;
+import org.nrg.xft.security.UserI;
+import org.nrg.xnat.services.PETTracerUtils;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+
+@Component
+public class GetSiteWidePETTracerList extends AbstractInitializingTask {
+ @Override
+ public String getTaskName() {
+ return "Get site-wide PET tracer list";
+ }
+
+ @Override
+ public void run() {
+ try {
+ final String path = PETTracerUtils.buildScriptPath(PETTracerUtils.ResourceScope.SITE_WIDE, "");
+ final Configuration configuration = PETTracerUtils.getService().getTracerList(path, null);
+ if (configuration == null) {
+ _log.info("Creating PET Tracer List.");
+ final String siteWide = FileUtils.readFileToString(PETTracerUtils.getDefaultTracerList());
+ final UserI adminUser = getAdminUser();
+ if (adminUser != null) {
+ PETTracerUtils.getService().setSiteWideTracerList(adminUser.getUsername(), path, siteWide);
+ } else {
+ throw new Exception("Site administrator not found.");
+ }
+ }
+ // there is a default site-wide tracer list, so nothing to do here for the else.
+ complete();
+ } catch (Throwable e){
+ _log.error("Unable to either find or initialize the PET tracer list.", e);
+ }
+ }
+
+ private UserI getAdminUser() throws Exception {
+ for (String login : Users.getAllLogins()) {
+ final UserI user = Users.getUser(login);
+ if (Roles.isSiteAdmin(user)) {
+ return user;
+ }
+ }
+ return null;
+ }
+
+ private static final Logger _log = LoggerFactory.getLogger(GetSiteWidePETTracerList.class);
+}
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/UpdateNewSecureDefinitions.java b/src/main/java/org/nrg/xnat/initialization/tasks/UpdateNewSecureDefinitions.java
new file mode 100644
index 00000000..357ee715
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/UpdateNewSecureDefinitions.java
@@ -0,0 +1,36 @@
+package org.nrg.xnat.initialization.tasks;
+
+import org.nrg.xdat.security.ElementSecurity;
+import org.nrg.xdat.security.services.FeatureRepositoryServiceI;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.stereotype.Component;
+
+@Component
+public class UpdateNewSecureDefinitions extends AbstractInitializingTask {
+ @Override
+ public String getTaskName() {
+ return "Update new secure definitions";
+ }
+
+ @Override
+ public void run() {
+ try {
+ if (ElementSecurity.GetElementSecurities() != null) {
+ _log.debug("Found element securities, running update new secure definitions.");
+ _featureRepositoryService.updateNewSecureDefinitions();
+ }
+ complete();
+ } catch (Exception ignore) {
+ // No worries...
+ }
+ }
+
+ private static final Logger _log = LoggerFactory.getLogger(UpdateNewSecureDefinitions.class);
+
+ @Autowired
+ @Lazy
+ private FeatureRepositoryServiceI _featureRepositoryService;
+}
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/UpdateUserAuthTable.java b/src/main/java/org/nrg/xnat/initialization/tasks/UpdateUserAuthTable.java
new file mode 100644
index 00000000..fd4cde90
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/UpdateUserAuthTable.java
@@ -0,0 +1,62 @@
+package org.nrg.xnat.initialization.tasks;
+
+import org.nrg.xdat.entities.XdatUserAuth;
+import org.nrg.xdat.services.XdatUserAuthService;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.jdbc.core.RowMapper;
+import org.springframework.security.core.authority.AuthorityUtils;
+import org.springframework.stereotype.Component;
+
+import java.sql.ResultSet;
+import java.sql.SQLException;
+import java.util.List;
+
+@Component
+public class UpdateUserAuthTable extends AbstractInitializingTask {
+ @Override
+ public String getTaskName() {
+ return "Update the user authentication table";
+ }
+
+ @Override
+ public void run() {
+ /**
+ * Adds users from /old xdat_user table to new user authentication table if they are not already there. New local database users now get added to both automatically, but this is necessary
+ * so that those who upgrade from an earlier version will still have their users be able to log in. Password expiry times are also added so that pre-existing users still have their passwords expire.
+ */
+ final List<XdatUserAuth> unmapped = _template.query("SELECT login, enabled FROM xdat_user WHERE login NOT IN (SELECT xdat_username FROM xhbm_xdat_user_auth)", new RowMapper<XdatUserAuth>() {
+ @Override
+ public XdatUserAuth mapRow(final ResultSet resultSet, final int i) throws SQLException {
+ final String login = resultSet.getString("login");
+ final boolean enabled = resultSet.getInt("enabled") == 1;
+ if (_log.isDebugEnabled()) {
+ _log.debug("Creating new user auth object for user {}, authentication is {}", login, enabled ? "enabled" : "disabled");
+ }
+ return new XdatUserAuth(login, XdatUserAuthService.LOCALDB, enabled, true, true, true, AuthorityUtils.NO_AUTHORITIES, login, 0);
+ }
+ });
+ for (XdatUserAuth userAuth : unmapped) {
+ if (_log.isDebugEnabled()) {
+ _log.debug("Persisting user auth object for user {}", userAuth.getXdatUsername());
+ }
+ _xdatUserAuthService.create(userAuth);
+ }
+ _log.debug("Updating the user auth table to set password updated to the current time for local users");
+ _template.execute("UPDATE xhbm_xdat_user_auth SET password_updated=current_timestamp WHERE auth_method='" + XdatUserAuthService.LOCALDB + "' AND password_updated IS NULL");
+ complete();
+ }
+
+ private static final Logger _log = LoggerFactory.getLogger(UpdateUserAuthTable.class);
+
+ @Autowired
+ @Lazy
+ private JdbcTemplate _template;
+
+ @Autowired
+ @Lazy
+ private XdatUserAuthService _xdatUserAuthService;
+}
diff --git a/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java b/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java
index 5763aa25..b73e8956 100644
--- a/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java
@@ -28,6 +28,7 @@ import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.ArcArchivespecificationNotificationTypeI;
import org.nrg.xdat.om.ArcArchivespecification;
import org.nrg.xdat.om.ArcArchivespecificationNotificationType;
+import org.nrg.xdat.preferences.SiteConfigPreferences;
import org.nrg.xdat.security.helpers.Roles;
import org.nrg.xdat.security.helpers.Users;
import org.nrg.xdat.turbine.utils.PopulateItem;
@@ -132,8 +133,10 @@ public class SettingsRestlet extends SecureResource {
private Map<Object, Object> getArcSpecAsMap() throws IOException, ConfigServiceException {
Map<Object, Object> settings = new HashMap<>();
+ final SiteConfigPreferences preferences = XDAT.getContextService().getBean(SiteConfigPreferences.class);
+
settings.putAll(XDAT.getSiteConfiguration());
- settings.put("siteId", getSiteId());
+ settings.put("siteId", preferences.getSiteTitle());
final String siteUrl = StringUtils.isBlank(_arcSpec.getSiteUrl()) ? XnatHttpUtils.getServerRoot(getHttpServletRequest()) : _arcSpec.getSiteUrl();
settings.put("siteUrl", siteUrl);
settings.put("siteAdminEmail", _arcSpec.getSiteAdminEmail());
@@ -168,18 +171,6 @@ public class SettingsRestlet extends SecureResource {
return settings;
}
- private String getSiteId() {
- String siteId = XFT.GetSiteID();
- if (StringUtils.isNotBlank(siteId)) {
- return siteId;
- }
- siteId = _arcSpec.getSiteId();
- if (StringUtils.isNotBlank(siteId)) {
- return siteId;
- }
- return XDAT.getContextService().getBean("siteId", String.class);
- }
-
private String emptyStringIfNull(final String configContents) {
return configContents == null ? "" : configContents;
}
diff --git a/src/main/java/org/nrg/xnat/restlet/servlet/XNATRestletServlet.java b/src/main/java/org/nrg/xnat/restlet/servlet/XNATRestletServlet.java
index 40a516aa..743892dc 100644
--- a/src/main/java/org/nrg/xnat/restlet/servlet/XNATRestletServlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/servlet/XNATRestletServlet.java
@@ -11,32 +11,15 @@
package org.nrg.xnat.restlet.servlet;
import com.noelios.restlet.ext.servlet.ServerServlet;
-import org.apache.commons.io.FileUtils;
-import org.nrg.config.entities.Configuration;
import org.nrg.dcm.DicomSCPManager;
import org.nrg.xdat.XDAT;
-import org.nrg.xdat.entities.XdatUserAuth;
-import org.nrg.xdat.security.helpers.Roles;
-import org.nrg.xdat.security.helpers.Users;
-import org.nrg.xdat.services.XdatUserAuthService;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.helpers.editscript.DicomEdit;
-import org.nrg.xnat.helpers.merge.AnonUtils;
import org.nrg.xnat.helpers.prearchive.PrearcConfig;
import org.nrg.xnat.helpers.prearchive.PrearcDatabase;
-import org.nrg.xnat.security.XnatPasswordEncrypter;
-import org.nrg.xnat.services.PETTracerUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
-import org.springframework.jdbc.core.JdbcTemplate;
-import org.springframework.jdbc.core.RowMapper;
-import org.springframework.security.core.authority.AuthorityUtils;
import javax.servlet.ServletConfig;
import javax.servlet.ServletException;
-import java.sql.ResultSet;
-import java.sql.SQLException;
-import java.util.List;
public class XNATRestletServlet extends ServerServlet {
private static final long serialVersionUID = -4149339105144231596L;
@@ -45,65 +28,11 @@ public class XNATRestletServlet extends ServerServlet {
private final Logger logger = LoggerFactory.getLogger(XNATRestletServlet.class);
- /**
- * Get the username of the site administrator. If there are multiple
- * site admins, just get the first one. If none are found, return null.
- * @return The name of the admin user.
- */
- @SuppressWarnings("unchecked")
- private String getAdminUser() throws Exception {
- for (String login : Users.getAllLogins()) {
- final UserI user = Users.getUser(login);
- if (Roles.isSiteAdmin(user)) {
- return login;
- }
- }
- return null;
- }
-
@Override
public void init() throws ServletException {
super.init();
- updateAuthTable();
-
XNATRestletServlet.REST_CONFIG=this.getServletConfig();
- try {
- String path = DicomEdit.buildScriptPath(DicomEdit.ResourceScope.SITE_WIDE, "");
- Configuration init_config = AnonUtils.getService().getScript(path, null);
- if (init_config == null) {
- logger.info("Creating Script Table.");
- String site_wide = FileUtils.readFileToString(AnonUtils.getDefaultScript());
- String adminUser = this.getAdminUser();
- if (adminUser != null) {
- AnonUtils.getService().setSiteWideScript(adminUser, path,site_wide);
- } else {
- throw new Exception("Site administrator not found.");
- }
- }
- // there is a default site-wide script, so nothing to do here for the else.
- } catch (Throwable e){
- logger.error("Unable to either find or initialize script database", e);
- }
-
- // blatant copy of how we initialize the anon script
- try {
- String path = PETTracerUtils.buildScriptPath(PETTracerUtils.ResourceScope.SITE_WIDE, "");
- Configuration init_config = PETTracerUtils.getService().getTracerList(path, null);
- if (init_config == null) {
- logger.info("Creating PET Tracer List.");
- String site_wide = FileUtils.readFileToString(PETTracerUtils.getDefaultTracerList());
- String adminUser = this.getAdminUser();
- if (adminUser != null) {
- PETTracerUtils.getService().setSiteWideTracerList(adminUser, path, site_wide);
- } else {
- throw new Exception("Site administrator not found.");
- }
- }
- // there is a default site-wide tracer list, so nothing to do here for the else.
- } catch (Throwable e){
- logger.error("Unable to either find or initialize the PET tracer list.", e);
- }
PrearcConfig prearcConfig = XDAT.getContextService().getBean(PrearcConfig.class);
try {
@@ -112,32 +41,9 @@ public class XNATRestletServlet extends ServerServlet {
logger.error("Unable to initialize prearchive database", e);
}
- XnatPasswordEncrypter.execute();
-
XDAT.getContextService().getBean(DicomSCPManager.class).startOrStopDicomSCPAsDictatedByConfiguration();
}
-
- /**
- * Adds users from /old xdat_user table to new user authentication table if they are not already there. New local database users now get added to both automatically, but this is necessary
- * so that those who upgrade from an earlier version will still have their users be able to log in. Password expiry times are also added so that pre-existing users still have their passwords expire.
- */
- private void updateAuthTable(){
- JdbcTemplate template = new JdbcTemplate(XDAT.getDataSource());
- List<XdatUserAuth> unmapped = template.query("SELECT login, enabled FROM xdat_user WHERE login NOT IN (SELECT xdat_username FROM xhbm_xdat_user_auth)", new RowMapper<XdatUserAuth>() {
- @Override
- public XdatUserAuth mapRow(final ResultSet resultSet, final int i) throws SQLException {
- final String login = resultSet.getString("login");
- final boolean enabled = resultSet.getInt("enabled") == 1;
- return new XdatUserAuth(login, XdatUserAuthService.LOCALDB, enabled, true, true, true, AuthorityUtils.NO_AUTHORITIES, login,0);
- }
- });
- for (XdatUserAuth userAuth : unmapped) {
- XDAT.getXdatUserAuthService().create(userAuth);
- }
- template.execute("UPDATE xhbm_xdat_user_auth SET password_updated=current_timestamp WHERE auth_method='"+XdatUserAuthService.LOCALDB+"' AND password_updated IS NULL");
- }
-
@Override
public void destroy() {
XDAT.getContextService().getBean(DicomSCPManager.class).stopDicomSCPs();
diff --git a/src/main/java/org/nrg/xnat/security/FilterSecurityInterceptorBeanPostProcessor.java b/src/main/java/org/nrg/xnat/security/FilterSecurityInterceptorBeanPostProcessor.java
index bd43be4b..78b409aa 100644
--- a/src/main/java/org/nrg/xnat/security/FilterSecurityInterceptorBeanPostProcessor.java
+++ b/src/main/java/org/nrg/xnat/security/FilterSecurityInterceptorBeanPostProcessor.java
@@ -10,12 +10,9 @@
*/
package org.nrg.xnat.security;
-import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
-import org.nrg.framework.constants.Scope;
-import org.nrg.prefs.entities.Preference;
-import org.nrg.prefs.services.PreferenceService;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.springframework.beans.BeansException;
import org.springframework.beans.factory.config.BeanPostProcessor;
import org.springframework.security.access.ConfigAttribute;
@@ -52,7 +49,7 @@ public class FilterSecurityInterceptorBeanPostProcessor implements BeanPostProce
if (bean instanceof FilterSecurityInterceptor) {
FilterSecurityInterceptor interceptor = (FilterSecurityInterceptor) bean;
- final ExpressionBasedFilterInvocationSecurityMetadataSource metadataSource = getMetadataSource(isRequiredLogin());
+ final ExpressionBasedFilterInvocationSecurityMetadataSource metadataSource = getMetadataSource(_service.getRequireLogin());
if (_log.isDebugEnabled()) {
_log.debug("Found a FilterSecurityInterceptor bean with the following metadata configuration:");
displayMetadataSource(interceptor.getSecurityMetadataSource());
@@ -106,20 +103,6 @@ public class FilterSecurityInterceptorBeanPostProcessor implements BeanPostProce
}
}
- private boolean isRequiredLogin() {
- final Preference preference = _service.getPreference("system", "require_login", Scope.Site, null);
- if (preference == null) {
- _log.warn("There is no preference set for the require_login setting.");
- return true;
- }
- final String value = preference.getValue();
- if (StringUtils.isBlank(value)) {
- _log.warn("There is no preference value set for the require_login setting.");
- return true;
- }
- return Boolean.parseBoolean(value);
- }
-
private static final Log _log = LogFactory.getLog(FilterSecurityInterceptorBeanPostProcessor.class);
private static final String PERMIT_ALL = "permitAll";
private static final String DEFAULT_PATTERN = "/**";
@@ -127,7 +110,7 @@ public class FilterSecurityInterceptorBeanPostProcessor implements BeanPostProce
private static final String DEFAULT_EXPRESSION = "hasRole('ROLE_USER')";
@Inject
- private PreferenceService _service;
+ private InitializerSiteConfiguration _service;
private final List<String> _openUrls = new ArrayList<>();
private final List<String> _adminUrls = new ArrayList<>();
diff --git a/src/main/java/org/nrg/xnat/security/ResetFailedLogins.java b/src/main/java/org/nrg/xnat/security/ResetFailedLogins.java
index d2bf58ae..9ca3f130 100644
--- a/src/main/java/org/nrg/xnat/security/ResetFailedLogins.java
+++ b/src/main/java/org/nrg/xnat/security/ResetFailedLogins.java
@@ -14,25 +14,27 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.jdbc.core.JdbcTemplate;
-import javax.inject.Inject;
-import javax.sql.DataSource;
-import java.util.concurrent.Callable;
-
public class ResetFailedLogins implements Runnable {
- public ResetFailedLogins(final DataSource dataSource) {
- _dataSource = dataSource;
+ public ResetFailedLogins(final JdbcTemplate template, final String interval) {
+ _template = template;
+ _interval = interval;
}
@Override
public void run() {
- JdbcTemplate template = new JdbcTemplate(_dataSource);
- template.execute("UPDATE xhbm_xdat_user_auth SET failed_login_attempts=0");
- _log.info("Reset all failed login attempts.");
+ if (_template.queryForObject("SELECT count(*) from xhbm_xdat_user_auth", Integer.TYPE) > 0) {
+ final int updated = _template.update("UPDATE xhbm_xdat_user_auth SET failed_login_attempts = 0 WHERE failed_login_attempts > 0 AND last_login_attempt < NOW() - INTERVAL '" + _interval + "'");
+ if (_log.isInfoEnabled()) {
+ _log.info("Reset {} failed login attempts.", updated);
+ }
+ } else {
+ _log.info("Didn't reset any failed login attempts, there's no data in the relevant table.");
+ }
}
private static final Logger _log = LoggerFactory.getLogger(ResetFailedLogins.class);
- private final DataSource _dataSource;
+ private final JdbcTemplate _template;
+ private final String _interval;
}
-
diff --git a/src/main/java/org/nrg/xnat/security/XnatExpiredPasswordFilter.java b/src/main/java/org/nrg/xnat/security/XnatExpiredPasswordFilter.java
index 845c9706..2dbbd476 100644
--- a/src/main/java/org/nrg/xnat/security/XnatExpiredPasswordFilter.java
+++ b/src/main/java/org/nrg/xnat/security/XnatExpiredPasswordFilter.java
@@ -10,22 +10,21 @@
*/
package org.nrg.xnat.security;
-import org.apache.commons.lang3.BooleanUtils;
import org.apache.commons.lang3.StringUtils;
import org.nrg.config.exceptions.SiteConfigurationException;
-import org.nrg.config.services.SiteConfigurationService;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.entities.AliasToken;
import org.nrg.xdat.entities.UserRole;
import org.nrg.xdat.om.ArcArchivespecification;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.nrg.xdat.security.helpers.Roles;
import org.nrg.xdat.services.AliasTokenService;
import org.nrg.xdat.services.XdatUserAuthService;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jdbc.core.RowMapper;
import org.springframework.security.crypto.codec.Base64;
@@ -44,9 +43,11 @@ import java.net.URI;
import java.net.URISyntaxException;
import java.sql.ResultSet;
import java.sql.SQLException;
+import java.text.SimpleDateFormat;
+import java.util.Date;
import java.util.List;
-
+@SuppressWarnings({"SqlDialectInspection", "SqlNoDataSourceInspection"})
public class XnatExpiredPasswordFilter extends GenericFilterBean {
private String changePasswordPath = "";
private String changePasswordDestination = "";
@@ -132,7 +133,12 @@ public class XnatExpiredPasswordFilter extends GenericFilterBean {
logger.error(e);
}
- if (isPasswordExpirationDisabled()) {
+ try {
+ passwordExpirationDisabled = isPasswordExpirationDisabled();
+ } catch (SiteConfigurationException e) {
+ logger.error("An error occurred trying to check for expired passwords, continuing processing.", e);
+ }
+ if (passwordExpirationDisabled) {
chain.doFilter(request, response);
} else {
final boolean isExpired = checkForExpiredPassword(username);
@@ -177,7 +183,7 @@ public class XnatExpiredPasswordFilter extends GenericFilterBean {
} else if (user.isEnabled()) {
boolean isExpired = checkForExpiredPassword(user);
- if ((!isUserNonExpiring(user) && isExpired) || (getBoolSiteConfigurationProperty("requireSaltedPasswords", true) && user.getSalt() == null)) {
+ if ((!isUserNonExpiring(user) && isExpired) || (_preferences.getRequireSaltedPasswords() && user.getSalt() == null)) {
request.getSession().setAttribute("expired", isExpired);
response.sendRedirect(TurbineUtils.GetFullServerPath() + changePasswordPath);
} else {
@@ -191,20 +197,6 @@ public class XnatExpiredPasswordFilter extends GenericFilterBean {
}
}
- private String getSiteConfigurationProperty(final String property) {
- try {
- return _siteConfigurationService.getSiteConfigurationProperty(property);
- } catch (SiteConfigurationException e) {
- _log.warn("An error occurred retrieving the site configuration property " + property, e);
- return null;
- }
- }
-
- private boolean getBoolSiteConfigurationProperty(final String property, final boolean _default) {
- final String value = getSiteConfigurationProperty(property);
- return StringUtils.isBlank(value) ? _default : BooleanUtils.toBoolean(value);
- }
-
public void setChangePasswordPath(String path) {
this.changePasswordPath = path;
}
@@ -271,14 +263,14 @@ public class XnatExpiredPasswordFilter extends GenericFilterBean {
return false;
}
if (isPasswordExpirationInterval()) {
- List<Boolean> expired = (new JdbcTemplate(_dataSource)).query("SELECT ((now()-password_updated)> (Interval '" + getPasswordExpirationSetting() + " days')) AS expired FROM xhbm_xdat_user_auth WHERE auth_user = ? AND auth_method = 'localdb'", new String[]{username}, new RowMapper<Boolean>() {
+ List<Boolean> expired = (new JdbcTemplate(_dataSource)).query("SELECT ((now()-password_updated)> (Interval '" + passwordExpirationSetting + " days')) AS expired FROM xhbm_xdat_user_auth WHERE auth_user = ? AND auth_method = 'localdb'", new String[]{username}, new RowMapper<Boolean>() {
public Boolean mapRow(ResultSet rs, int rowNum) throws SQLException {
return rs.getBoolean(1);
}
});
return expired.get(0);
} else {
- List<Boolean> expired = (new JdbcTemplate(_dataSource)).query("SELECT (to_date('" + getPasswordExpirationSetting() + "', 'MM/DD/YYYY') BETWEEN password_updated AND now()) AS expired FROM xhbm_xdat_user_auth WHERE auth_user = ? AND auth_method = 'localdb'", new String[]{username}, new RowMapper<Boolean>() {
+ List<Boolean> expired = (new JdbcTemplate(_dataSource)).query("SELECT (to_date('" + new SimpleDateFormat("MM/dd/yyyy").format(new Date(Long.parseLong(passwordExpirationSetting))) + "', 'MM/DD/YYYY') BETWEEN password_updated AND now()) AS expired FROM xhbm_xdat_user_auth WHERE auth_user = ? AND auth_method = 'localdb'", new String[]{username}, new RowMapper<Boolean>() {
public Boolean mapRow(ResultSet rs, int rowNum) throws SQLException {
return rs.getBoolean(1);
}
@@ -291,20 +283,20 @@ public class XnatExpiredPasswordFilter extends GenericFilterBean {
return false;
}
- private boolean isPasswordExpirationDisabled() {
+ private boolean isPasswordExpirationDisabled() throws SiteConfigurationException {
if (!passwordExpirationDirtied) {
return passwordExpirationDisabled;
}
- final String type = getSiteConfigurationProperty("passwordExpirationType");
+ final String type = _preferences.getPasswordExpirationType();
if (StringUtils.isBlank(type)) {
passwordExpirationDisabled = true;
} else if (type.equals("Interval")) {
passwordExpirationInterval = true;
- passwordExpirationSetting = validatePasswordExpirationInterval(getSiteConfigurationProperty("passwordExpirationInterval"));
+ passwordExpirationSetting = Integer.toString(_preferences.getPasswordExpirationInterval());
passwordExpirationDisabled = passwordExpirationSetting.equals("0");
} else if (type.equals("Date")) {
passwordExpirationInterval = false;
- passwordExpirationSetting = validatePasswordExpirationDate(getSiteConfigurationProperty("passwordExpirationDate"));
+ passwordExpirationSetting = Long.toString(_preferences.getPasswordExpirationDate().getTime());
passwordExpirationDisabled = passwordExpirationSetting.equals("0");
} else {
passwordExpirationDisabled = true;
@@ -313,25 +305,10 @@ public class XnatExpiredPasswordFilter extends GenericFilterBean {
return passwordExpirationDisabled;
}
- private String validatePasswordExpirationInterval(final String passwordExpirationInterval) {
- // overly long intervals break the query; this limit allows intervals up to approximately 2700 years, which should be sufficient for most purposes
- return StringUtils.isNotBlank(passwordExpirationInterval) && !passwordExpirationInterval.equals("0") && passwordExpirationInterval.length() <= 6 && passwordExpirationInterval.matches("\\d+") ?
- passwordExpirationInterval : "0";
- }
-
- private String validatePasswordExpirationDate(final String passwordExpirationDate) {
- return StringUtils.isNotBlank(passwordExpirationDate) && passwordExpirationDate.matches("\\d\\d/\\d\\d/\\d\\d\\d\\d")
- ? passwordExpirationDate : "0";
- }
-
private boolean isPasswordExpirationInterval() {
return passwordExpirationInterval;
}
- private String getPasswordExpirationSetting() {
- return passwordExpirationSetting;
- }
-
private boolean isUserNonExpiring(UserI user) {
try {
return Roles.checkRole(user, UserRole.ROLE_NON_EXPIRING);
@@ -350,12 +327,12 @@ public class XnatExpiredPasswordFilter extends GenericFilterBean {
}
}
- private static final Logger _log = LoggerFactory.getLogger(XnatExpiredPasswordFilter.class);
-
- @Inject
- private SiteConfigurationService _siteConfigurationService;
+ @Autowired
+ @Lazy
+ private InitializerSiteConfiguration _preferences;
- @Inject
+ @Autowired
+ @Lazy
private AliasTokenService _aliasTokenService;
@Inject
diff --git a/src/main/java/org/nrg/xnat/security/XnatLdapUserDetailsMapper.java b/src/main/java/org/nrg/xnat/security/XnatLdapUserDetailsMapper.java
index c23f9b4d..cbced69c 100644
--- a/src/main/java/org/nrg/xnat/security/XnatLdapUserDetailsMapper.java
+++ b/src/main/java/org/nrg/xnat/security/XnatLdapUserDetailsMapper.java
@@ -12,7 +12,7 @@ package org.nrg.xnat.security;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
-import org.nrg.config.services.SiteConfigurationService;
+import org.nrg.xdat.preferences.SiteConfigPreferences;
import org.nrg.xdat.security.helpers.Users;
import org.nrg.xdat.services.XdatUserAuthService;
import org.nrg.xft.security.UserI;
@@ -22,7 +22,6 @@ import org.springframework.security.core.userdetails.UserDetails;
import org.springframework.security.ldap.userdetails.LdapUserDetailsMapper;
import org.springframework.util.Assert;
-import javax.inject.Inject;
import java.util.Collection;
import java.util.HashMap;
import java.util.Map;
@@ -30,11 +29,11 @@ import java.util.Map;
public class XnatLdapUserDetailsMapper extends LdapUserDetailsMapper {
public static final String PROPERTY_PREFIX = "attributes.";
- public static final String PROPERTY_EMAIL = PROPERTY_PREFIX + "email";
- public static final String PROPERTY_FIRST = PROPERTY_PREFIX + "firstname";
- public static final String PROPERTY_LAST = PROPERTY_PREFIX + "lastname";
+ public static final String PROPERTY_EMAIL = PROPERTY_PREFIX + "email";
+ public static final String PROPERTY_FIRST = PROPERTY_PREFIX + "firstname";
+ public static final String PROPERTY_LAST = PROPERTY_PREFIX + "lastname";
- public XnatLdapUserDetailsMapper(final String authMethodId, final Map<String, String> properties) {
+ public XnatLdapUserDetailsMapper(final String authMethodId, final Map<String, String> properties, final XdatUserAuthService userAuthService, final SiteConfigPreferences preferences) {
super();
Assert.hasText(authMethodId, "You must provide an authentication method ID.");
Assert.notEmpty(properties, "You must provide the authentication provider properties.");
@@ -60,6 +59,8 @@ public class XnatLdapUserDetailsMapper extends LdapUserDetailsMapper {
}
_properties = properties;
}
+ _userAuthService = userAuthService;
+ _preferences = preferences;
}
@Override
@@ -73,8 +74,8 @@ public class XnatLdapUserDetailsMapper extends LdapUserDetailsMapper {
UserI userDetails = _userAuthService.getUserDetailsByNameAndAuth(user.getUsername(), XdatUserAuthService.LDAP, _authMethodId, email, lastname, firstname);
try {
- UserI xdatUser = Users.getUser(userDetails.getUsername());
- if ((!_siteConfigurationService.getBoolSiteConfigurationProperty("emailVerification", false) || xdatUser.isVerified()) && userDetails.getAuthorization().isEnabled()) {
+ final UserI xdatUser = Users.getUser(userDetails.getUsername());
+ if ((!_preferences.getEmailVerification() || xdatUser.isVerified()) && userDetails.getAuthorization().isEnabled()) {
return userDetails;
} else {
throw new NewLdapAccountNotAutoEnabledException(
@@ -92,12 +93,8 @@ public class XnatLdapUserDetailsMapper extends LdapUserDetailsMapper {
private static final Log _log = LogFactory.getLog(XnatLdapUserDetailsMapper.class);
- @Inject
- private XdatUserAuthService _userAuthService;
-
- @Inject
- private SiteConfigurationService _siteConfigurationService;
-
- private final String _authMethodId;
- private final Map<String, String> _properties;
+ private final XdatUserAuthService _userAuthService;
+ private final SiteConfigPreferences _preferences;
+ private final String _authMethodId;
+ private final Map<String, String> _properties;
}
diff --git a/src/main/java/org/nrg/xnat/security/XnatPasswordEncrypter.java b/src/main/java/org/nrg/xnat/security/XnatPasswordEncrypter.java
deleted file mode 100644
index 3bb0feb4..00000000
--- a/src/main/java/org/nrg/xnat/security/XnatPasswordEncrypter.java
+++ /dev/null
@@ -1,71 +0,0 @@
-/*
- * org.nrg.xnat.security.XnatPasswordEncrypter
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 12/11/13 3:33 PM
- */
-package org.nrg.xnat.security;/*
- * org.nrg.xnat.helpers.prearchive.PrearcDatabase
- * XNAT http://www.xnat.org
- * Copyright (c) 2013, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Created 12/4/13 3:12 PM
- */
-
-import org.nrg.xft.db.PoolDBUtils;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.security.authentication.encoding.ShaPasswordEncoder;
-
-import java.sql.ResultSet;
-import java.util.HashMap;
-import java.util.Map;
-
-public class XnatPasswordEncrypter {
- private static Logger logger = LoggerFactory.getLogger(XnatPasswordEncrypter.class);
-
- public static void execute() {
- try {
- ShaPasswordEncoder encoder = new ShaPasswordEncoder(256);
-
- Map<Integer, String> userPasswords = new HashMap<Integer, String>();
- ResultSet rs= new PoolDBUtils().executeQuery(null, "SELECT xdat_user_id, primary_password FROM xdat_user WHERE primary_password IS NOT NULL AND length(primary_password) != 64", null);
- while(rs.next()){
- int id = rs.getInt(1);
- String password = rs.getString(2);
- String encodedPassword = encoder.encodePassword(password, null);
- userPasswords.put(id, encodedPassword);
- }
-
- Map<Integer, String> historyPasswords = new HashMap<Integer, String>();
- ResultSet rs2 = new PoolDBUtils().executeQuery(null, "SELECT history_id, primary_password FROM xdat_user_history WHERE primary_password IS NOT NULL AND length(primary_password) != 64", null);
- while(rs2.next()){
- int id = rs2.getInt(1);
- String password = rs2.getString(2);
- String encodedPassword = encoder.encodePassword(password, null);
- historyPasswords.put(id, encodedPassword);
- }
-
- for (int userId : userPasswords.keySet()) {
- new PoolDBUtils().executeNonSelectQuery("UPDATE xdat_user SET primary_password = '" + userPasswords.get(userId) + "' WHERE xdat_user_id = " + userId, null, null);
- }
-
- for (int historyId : historyPasswords.keySet()) {
- new PoolDBUtils().executeNonSelectQuery("UPDATE xdat_user_history SET primary_password = '" + historyPasswords.get(historyId) + "' WHERE history_id = " + historyId, null, null);
- }
-
- if (!userPasswords.isEmpty() || !historyPasswords.isEmpty()) {
- new PoolDBUtils().executeNonSelectQuery("DELETE FROM xs_item_cache", null, null);
- }
- } catch (Exception e) {
- logger.error("",e);
- }
- }
-}
diff --git a/src/main/java/org/nrg/xnat/security/XnatProviderManager.java b/src/main/java/org/nrg/xnat/security/XnatProviderManager.java
index 429e320f..6e1e149f 100644
--- a/src/main/java/org/nrg/xnat/security/XnatProviderManager.java
+++ b/src/main/java/org/nrg/xnat/security/XnatProviderManager.java
@@ -17,6 +17,7 @@ import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.apache.velocity.VelocityContext;
import org.hibernate.exception.DataException;
+import org.nrg.framework.services.ContextService;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.entities.AliasToken;
import org.nrg.xdat.entities.UserAuthI;
@@ -35,6 +36,9 @@ import org.nrg.xnat.security.provider.XnatLdapAuthenticationProvider;
import org.nrg.xnat.security.tokens.XnatDatabaseUsernamePasswordAuthenticationToken;
import org.nrg.xnat.security.tokens.XnatLdapUsernamePasswordAuthenticationToken;
import org.nrg.xnat.security.userdetailsservices.XnatDatabaseUserDetailsService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Lazy;
import org.springframework.context.support.MessageSourceAccessor;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jdbc.core.RowMapper;
@@ -81,9 +85,8 @@ public class XnatProviderManager extends ProviderManager {
// HACK: This is a hack to work around open XNAT auth issue. If this is a bare un/pw auth token, use anon auth.
if (authentication.getClass() == UsernamePasswordAuthenticationToken.class && authentication.getName().equalsIgnoreCase("guest")) {
-
- providers.add(_anonymousAuthenticationProvider);
- authentication = new AnonymousAuthenticationToken(_anonymousAuthenticationProvider.getKey(), authentication.getPrincipal(), Collections.<GrantedAuthority>singletonList(new SimpleGrantedAuthority("ROLE_ANONYMOUS")));
+ providers.add(getAnonymousAuthenticationProvider());
+ authentication = new AnonymousAuthenticationToken(getAnonymousAuthenticationProvider().getKey(), authentication.getPrincipal(), Collections.<GrantedAuthority>singletonList(new SimpleGrantedAuthority("ROLE_ANONYMOUS")));
} else {
for (AuthenticationProvider candidate : getProviders()) {
if (!candidate.supports(toTest)) {
@@ -169,6 +172,10 @@ public class XnatProviderManager extends ProviderManager {
}
}
+ private AnonymousAuthenticationProvider getAnonymousAuthenticationProvider() {
+ return _contextService.getBean(AnonymousAuthenticationProvider.class);
+ }
+
public void setProperties(List<String> fileNames) {
_properties = new Properties();
for (String filename : fileNames) {
@@ -184,7 +191,7 @@ public class XnatProviderManager extends ProviderManager {
}
}
- public static XdatUserAuth getUserByAuth(Authentication authentication) {
+ public XdatUserAuth getUserByAuth(Authentication authentication) {
if(authentication==null){
return null;
}
@@ -206,7 +213,7 @@ public class XnatProviderManager extends ProviderManager {
}
try {
- return XDAT.getXdatUserAuthService().getUserByNameAndAuth(u, method, provider);
+ return getUserAuthService().getUserByNameAndAuth(u, method, provider);
} catch (DataException exception) {
_log.error("An error occurred trying to retrieve the auth method", exception);
throw new RuntimeException("An error occurred trying to validate the given information. Please check your username and password. If this problem persists, please contact your system administrator.");
@@ -227,7 +234,7 @@ public class XnatProviderManager extends ProviderManager {
String auth = cached_methods.get(username);
if (auth == null) {
try {
- List<XdatUserAuth> userAuths = _service.getUsersByName(username);
+ List<XdatUserAuth> userAuths = getUserAuthService().getUsersByName(username);
if (userAuths.size() == 1) {
auth = userAuths.get(0).getAuthMethod();
cached_methods.put(username.intern(), auth.intern());
@@ -252,6 +259,13 @@ public class XnatProviderManager extends ProviderManager {
return auth;
}
+ private XdatUserAuthService getUserAuthService() {
+ if (_userAuthService == null) {
+ _userAuthService = _contextService.getBean(XdatUserAuthService.class);
+ }
+ return _userAuthService;
+ }
+
private static UsernamePasswordAuthenticationToken buildUPToken(XnatAuthenticationProvider provider, String username, String password){
if (provider instanceof XnatLdapAuthenticationProvider) {
return new XnatLdapUsernamePasswordAuthenticationToken(username, password, provider.getProviderId());
@@ -301,8 +315,13 @@ public class XnatProviderManager extends ProviderManager {
private static final class AuthenticationAttemptEventPublisher implements AuthenticationEventPublisher {
- private final FailedAttemptsManager failedAttemptsManager = new FailedAttemptsManager();
- private final LastSuccessfulLoginManager lastSuccessfulLoginManager = new LastSuccessfulLoginManager();
+ private final FailedAttemptsManager failedAttemptsManager;
+ private final LastSuccessfulLoginManager lastSuccessfulLoginManager;
+
+ private AuthenticationAttemptEventPublisher(final XnatProviderManager manager) {
+ failedAttemptsManager = new FailedAttemptsManager(manager);
+ lastSuccessfulLoginManager = new LastSuccessfulLoginManager(manager);
+ }
public void publishAuthenticationFailure(AuthenticationException exception, Authentication authentication) {
//increment failed login attempt
@@ -316,27 +335,41 @@ public class XnatProviderManager extends ProviderManager {
}
private static final class LastSuccessfulLoginManager {
+ private final XnatProviderManager _manager;
+
+ public LastSuccessfulLoginManager(final XnatProviderManager manager) {
+ _manager = manager;
+ }
+
private void updateLastSuccessfulLogin(Authentication auth) {
- XdatUserAuth ua = getUserByAuth(auth);
+ XdatUserAuth ua = _manager.getUserByAuth(auth);
if (ua != null) {
Date now = java.util.Calendar.getInstance(TimeZone.getDefault()).getTime();
ua.setLastSuccessfulLogin(now);
+ ua.setLastLoginAttempt(now);
XDAT.getXdatUserAuthService().update(ua);
}
}
}
private static final class FailedAttemptsManager {
+ private final XnatProviderManager _manager;
+
+ public FailedAttemptsManager(final XnatProviderManager manager) {
+ _manager = manager;
+ }
+
/**
* Increments failed Login count
*
* @param auth The authentication that failed.
*/
private synchronized void addFailedLoginAttempt(final Authentication auth) {
- XdatUserAuth ua = getUserByAuth(auth);
+ XdatUserAuth ua = _manager.getUserByAuth(auth);
if (ua != null) {
if (AuthUtils.MAX_FAILED_LOGIN_ATTEMPTS > 0) {
ua.setFailedLoginAttempts(ua.getFailedLoginAttempts() + 1);
+ ua.setLastLoginAttempt(new Date());
XDAT.getXdatUserAuthService().update(ua);
}
@@ -359,7 +392,7 @@ public class XnatProviderManager extends ProviderManager {
public void clearCount(final Authentication auth) {
if (AuthUtils.MAX_FAILED_LOGIN_ATTEMPTS > 0) {
- XdatUserAuth ua = getUserByAuth(auth);
+ XdatUserAuth ua = _manager.getUserByAuth(auth);
if (ua != null) {
ua.setFailedLoginAttempts(0);
XDAT.getXdatUserAuthService().update(ua);
@@ -382,14 +415,15 @@ public class XnatProviderManager extends ProviderManager {
protected MessageSourceAccessor messages = SpringSecurityMessageSource.getAccessor();
@Inject
- private XdatUserAuthService _service;
+ private DataSource _dataSource;
- @Inject
- private AnonymousAuthenticationProvider _anonymousAuthenticationProvider;
+ @Autowired
+ @Qualifier("rootContextService")
+ @Lazy
+ private ContextService _contextService;
- @Inject
- private DataSource _dataSource;
+ private XdatUserAuthService _userAuthService;
- private final AuthenticationEventPublisher eventPublisher = new AuthenticationAttemptEventPublisher();
+ private final AuthenticationEventPublisher eventPublisher = new AuthenticationAttemptEventPublisher(this);
private Properties _properties;
}
diff --git a/src/main/java/org/nrg/xnat/security/alias/AliasTokenAuthenticationProvider.java b/src/main/java/org/nrg/xnat/security/alias/AliasTokenAuthenticationProvider.java
index 37e51060..bce95af4 100644
--- a/src/main/java/org/nrg/xnat/security/alias/AliasTokenAuthenticationProvider.java
+++ b/src/main/java/org/nrg/xnat/security/alias/AliasTokenAuthenticationProvider.java
@@ -17,6 +17,8 @@ import org.nrg.xdat.services.AliasTokenService;
import org.nrg.xdat.services.XdatUserAuthService;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.security.provider.XnatAuthenticationProvider;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
import org.springframework.security.authentication.AuthenticationServiceException;
import org.springframework.security.authentication.BadCredentialsException;
import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
@@ -176,10 +178,12 @@ public class AliasTokenAuthenticationProvider extends AbstractUserDetailsAuthent
return _userAuthService.getUserDetailsByUsernameAndMostRecentSuccessfulLogin(token.getXdatUserId());
}
- @Inject
+ @Autowired
+ @Lazy
private AliasTokenService _aliasTokenService;
- @Inject
+ @Autowired
+ @Lazy
private XdatUserAuthService _userAuthService;
private String _name;
diff --git a/src/main/java/org/nrg/xnat/security/alias/ClearExpiredAliasTokens.java b/src/main/java/org/nrg/xnat/security/alias/ClearExpiredAliasTokens.java
index 5d8067cf..cb1ed6fc 100644
--- a/src/main/java/org/nrg/xnat/security/alias/ClearExpiredAliasTokens.java
+++ b/src/main/java/org/nrg/xnat/security/alias/ClearExpiredAliasTokens.java
@@ -14,17 +14,16 @@ import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.jdbc.core.JdbcTemplate;
-import javax.sql.DataSource;
import java.util.Arrays;
import java.util.List;
public class ClearExpiredAliasTokens implements Runnable {
- public ClearExpiredAliasTokens(final DataSource dataSource, final String timeout) {
+ public ClearExpiredAliasTokens(final JdbcTemplate template, final String timeout) {
if (_log.isDebugEnabled()) {
_log.debug("Initializing the alias token sweeper job with an interval of: " + timeout);
}
- _dataSource = dataSource;
+ _template = template;
_timeout = timeout;
}
@@ -35,13 +34,12 @@ public class ClearExpiredAliasTokens implements Runnable {
if (_log.isDebugEnabled()) {
_log.debug("Executing alias token sweep function");
}
- JdbcTemplate template = new JdbcTemplate(_dataSource);
for (final String format : ALIAS_TOKEN_QUERIES) {
final String query = String.format(format, _timeout);
if (_log.isDebugEnabled()) {
_log.debug("Executing alias token sweep query: " + query);
}
- template.execute(query);
+ _template.execute(query);
}
}
@@ -50,6 +48,6 @@ public class ClearExpiredAliasTokens implements Runnable {
private static final String QUERY_DELETE_ALIAS_TOKENS = "DELETE FROM xhbm_alias_token WHERE created < NOW() - INTERVAL '%s'";
private static final List<String> ALIAS_TOKEN_QUERIES = Arrays.asList(QUERY_DELETE_TOKEN_IP_ADDRESSES, QUERY_DELETE_ALIAS_TOKENS);
- private final DataSource _dataSource;
- private final String _timeout;
+ private final JdbcTemplate _template;
+ private final String _timeout;
}
diff --git a/src/main/java/org/nrg/xnat/security/config/DatabaseAuthenticationProviderConfigurator.java b/src/main/java/org/nrg/xnat/security/config/DatabaseAuthenticationProviderConfigurator.java
index 4b6eecb3..3f338a30 100644
--- a/src/main/java/org/nrg/xnat/security/config/DatabaseAuthenticationProviderConfigurator.java
+++ b/src/main/java/org/nrg/xnat/security/config/DatabaseAuthenticationProviderConfigurator.java
@@ -10,15 +10,16 @@
*/
package org.nrg.xnat.security.config;
-import org.nrg.config.services.SiteConfigurationService;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.nrg.xdat.security.ObfuscatedPasswordEncoder;
import org.nrg.xnat.security.provider.XnatDatabaseAuthenticationProvider;
import org.nrg.xnat.security.userdetailsservices.XnatDatabaseUserDetailsService;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
import org.springframework.security.authentication.AuthenticationProvider;
import org.springframework.security.authentication.dao.ReflectionSaltSource;
import org.springframework.security.authentication.encoding.ShaPasswordEncoder;
-import javax.inject.Inject;
import java.util.ArrayList;
import java.util.List;
import java.util.Map;
@@ -31,7 +32,7 @@ public class DatabaseAuthenticationProviderConfigurator extends AbstractAuthenti
ReflectionSaltSource saltSource = new ReflectionSaltSource();
saltSource.setUserPropertyToUse("salt");
- XnatDatabaseAuthenticationProvider sha2DatabaseAuthProvider = new XnatDatabaseAuthenticationProvider(_siteConfigurationService);
+ XnatDatabaseAuthenticationProvider sha2DatabaseAuthProvider = new XnatDatabaseAuthenticationProvider(_preferences.getEmailVerification());
ShaPasswordEncoder encoder = new ShaPasswordEncoder(256);
sha2DatabaseAuthProvider.setUserDetailsService(_detailsService);
sha2DatabaseAuthProvider.setPasswordEncoder(encoder);
@@ -40,7 +41,7 @@ public class DatabaseAuthenticationProviderConfigurator extends AbstractAuthenti
sha2DatabaseAuthProvider.setSaltSource(saltSource);
providers.add(sha2DatabaseAuthProvider);
- XnatDatabaseAuthenticationProvider sha2ObfuscatedDatabaseAuthProvider = new XnatDatabaseAuthenticationProvider(_siteConfigurationService);
+ XnatDatabaseAuthenticationProvider sha2ObfuscatedDatabaseAuthProvider = new XnatDatabaseAuthenticationProvider(_preferences.getEmailVerification());
ObfuscatedPasswordEncoder encoder2 = new ObfuscatedPasswordEncoder(256);
sha2ObfuscatedDatabaseAuthProvider.setUserDetailsService(_detailsService);
sha2ObfuscatedDatabaseAuthProvider.setPasswordEncoder(encoder2);
@@ -57,11 +58,10 @@ public class DatabaseAuthenticationProviderConfigurator extends AbstractAuthenti
return getAuthenticationProviders(id, name);
}
- @Inject
+ @Autowired
+ @Lazy
private XnatDatabaseUserDetailsService _detailsService;
- @Inject
- private SiteConfigurationService _siteConfigurationService;
-
-
+ @Autowired
+ private InitializerSiteConfiguration _preferences;
}
diff --git a/src/main/java/org/nrg/xnat/security/config/LdapAuthenticationProviderConfigurator.java b/src/main/java/org/nrg/xnat/security/config/LdapAuthenticationProviderConfigurator.java
index 874b2d0d..b0e535b1 100644
--- a/src/main/java/org/nrg/xnat/security/config/LdapAuthenticationProviderConfigurator.java
+++ b/src/main/java/org/nrg/xnat/security/config/LdapAuthenticationProviderConfigurator.java
@@ -13,9 +13,13 @@ package org.nrg.xnat.security.config;
import org.apache.commons.lang3.NotImplementedException;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.nrg.xdat.preferences.SiteConfigPreferences;
+import org.nrg.xdat.services.XdatUserAuthService;
import org.nrg.xnat.security.XnatLdapAuthoritiesPopulator;
import org.nrg.xnat.security.XnatLdapUserDetailsMapper;
import org.nrg.xnat.security.provider.XnatLdapAuthenticationProvider;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.context.annotation.Lazy;
import org.springframework.security.authentication.AuthenticationProvider;
import org.springframework.security.ldap.DefaultSpringSecurityContextSource;
import org.springframework.security.ldap.authentication.BindAuthenticator;
@@ -35,7 +39,7 @@ public class LdapAuthenticationProviderConfigurator extends AbstractAuthenticati
public List<AuthenticationProvider> getAuthenticationProviders(String id, String name, Map<String, String> properties) {
try {
XnatLdapAuthenticationProvider ldapAuthProvider = new XnatLdapAuthenticationProvider(getBindAuthenticator(properties, getLdapContextSource(properties)), new XnatLdapAuthoritiesPopulator());
- ldapAuthProvider.setUserDetailsContextMapper(new XnatLdapUserDetailsMapper(id, properties));
+ ldapAuthProvider.setUserDetailsContextMapper(new XnatLdapUserDetailsMapper(id, properties, _userAuthService, _preferences));
ldapAuthProvider.setName(name);
ldapAuthProvider.setProviderId(id);
return Arrays.asList(new AuthenticationProvider[] { ldapAuthProvider });
@@ -60,4 +64,12 @@ public class LdapAuthenticationProviderConfigurator extends AbstractAuthenticati
}
private static final Log _log = LogFactory.getLog(LdapAuthenticationProviderConfigurator.class);
+
+ @Autowired
+ @Lazy
+ private XdatUserAuthService _userAuthService;
+
+ @Autowired
+ @Lazy
+ private SiteConfigPreferences _preferences;
}
diff --git a/src/main/java/org/nrg/xnat/security/provider/XnatDatabaseAuthenticationProvider.java b/src/main/java/org/nrg/xnat/security/provider/XnatDatabaseAuthenticationProvider.java
index cef069f4..ed43dced 100644
--- a/src/main/java/org/nrg/xnat/security/provider/XnatDatabaseAuthenticationProvider.java
+++ b/src/main/java/org/nrg/xnat/security/provider/XnatDatabaseAuthenticationProvider.java
@@ -10,17 +10,11 @@
*/
package org.nrg.xnat.security.provider;
-import org.nrg.config.services.SiteConfigurationService;
import org.nrg.xdat.services.XdatUserAuthService;
import org.nrg.xft.db.PoolDBUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.security.tokens.XnatDatabaseUsernamePasswordAuthenticationToken;
-import org.springframework.security.authentication.AccountExpiredException;
-import org.springframework.security.authentication.AuthenticationServiceException;
-import org.springframework.security.authentication.CredentialsExpiredException;
-import org.springframework.security.authentication.DisabledException;
-import org.springframework.security.authentication.LockedException;
-import org.springframework.security.authentication.UsernamePasswordAuthenticationToken;
+import org.springframework.security.authentication.*;
import org.springframework.security.authentication.dao.DaoAuthenticationProvider;
import org.springframework.security.authentication.encoding.PlaintextPasswordEncoder;
import org.springframework.security.core.AuthenticationException;
@@ -29,9 +23,9 @@ import org.springframework.security.core.userdetails.UserDetailsChecker;
public class XnatDatabaseAuthenticationProvider extends DaoAuthenticationProvider implements XnatAuthenticationProvider {
- public XnatDatabaseAuthenticationProvider(final SiteConfigurationService siteConfigurationService) {
+ public XnatDatabaseAuthenticationProvider(final boolean requireEmailVerification) {
super();
- _siteConfigurationService = siteConfigurationService;
+ _requireEmailVerification = requireEmailVerification;
this.setPreAuthenticationChecks(new PreAuthenticationChecks());
}
@@ -85,7 +79,7 @@ public class XnatDatabaseAuthenticationProvider extends DaoAuthenticationProvide
throw new AuthenticationServiceException("User details class is not of a type I know how to handle: " + userDetails.getClass());
}
final UserI xdatUserDetails = (UserI) userDetails;
- if ((_siteConfigurationService.getBoolSiteConfigurationProperty("emailVerification", false) && !xdatUserDetails.isVerified() && xdatUserDetails.isEnabled()) || !xdatUserDetails.isAccountNonLocked()) {
+ if ((_requireEmailVerification && !xdatUserDetails.isVerified() && xdatUserDetails.isEnabled()) || !xdatUserDetails.isAccountNonLocked()) {
throw new CredentialsExpiredException("Attempted login to unverified or locked account: " + xdatUserDetails.getUsername());
}
super.additionalAuthenticationChecks(userDetails, authentication);
@@ -95,8 +89,6 @@ public class XnatDatabaseAuthenticationProvider extends DaoAuthenticationProvide
return (this.getPasswordEncoder().getClass() == plainText);
}
- private final SiteConfigurationService _siteConfigurationService;
-
private String displayName = "";
private String _providerId = "";
private Class plainText = PlaintextPasswordEncoder.class;
@@ -148,4 +140,6 @@ public class XnatDatabaseAuthenticationProvider extends DaoAuthenticationProvide
return false;
}
}
+
+ private final boolean _requireEmailVerification;
}
diff --git a/src/main/java/org/nrg/xnat/security/userdetailsservices/XnatDatabaseUserDetailsService.java b/src/main/java/org/nrg/xnat/security/userdetailsservices/XnatDatabaseUserDetailsService.java
index 0dc6d84b..a69154c7 100644
--- a/src/main/java/org/nrg/xnat/security/userdetailsservices/XnatDatabaseUserDetailsService.java
+++ b/src/main/java/org/nrg/xnat/security/userdetailsservices/XnatDatabaseUserDetailsService.java
@@ -1,43 +1,54 @@
/*
- * org.nrg.xnat.security.userdetailsservices.XnatDatabaseUserDetailsService
+ * XnatDatabaseUserDetailsService
* XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
+ * Copyright (c) 2016, Washington University School of Medicine
* All Rights Reserved
*
* Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
*/
package org.nrg.xnat.security.userdetailsservices;
+import org.nrg.framework.services.ContextService;
import org.nrg.xdat.services.XdatUserAuthService;
import org.nrg.xnat.security.PasswordExpiredException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.beans.factory.annotation.Qualifier;
+import org.springframework.context.annotation.Lazy;
import org.springframework.dao.DataAccessException;
import org.springframework.security.core.userdetails.UserDetails;
import org.springframework.security.core.userdetails.UserDetailsService;
import org.springframework.security.core.userdetails.UsernameNotFoundException;
import org.springframework.security.core.userdetails.jdbc.JdbcDaoImpl;
-import javax.inject.Inject;
-
public class XnatDatabaseUserDetailsService extends JdbcDaoImpl implements UserDetailsService {
// MIGRATION: This needs to go away and be replaced by a standard property for an XNAT user details service.
- public static final String DB_PROVIDER = "";
-
- @Override
+ public static final String DB_PROVIDER = "";
+
+ @Override
public UserDetails loadUserByUsername(String username) throws UsernameNotFoundException, DataAccessException, PasswordExpiredException {
- UserDetails user = _service.getUserDetailsByNameAndAuth(username, XdatUserAuthService.LOCALDB, DB_PROVIDER);
+ UserDetails user = getXdatUserAuthService().getUserDetailsByNameAndAuth(username, XdatUserAuthService.LOCALDB, DB_PROVIDER);
if (_log.isDebugEnabled()) {
_log.debug("Loaded user {} by username from user-auth service.", user.getUsername());
}
return user;
}
+ private XdatUserAuthService getXdatUserAuthService() {
+ if (_xdatUserAuthService == null) {
+ _xdatUserAuthService = _contextService.getBean(XdatUserAuthService.class);
+ }
+ return _xdatUserAuthService;
+ }
+
private static final Logger _log = LoggerFactory.getLogger(XnatDatabaseUserDetailsService.class);
- @Inject
- private XdatUserAuthService _service;
+ @Autowired
+ @Qualifier("rootContextService")
+ @Lazy
+ private ContextService _contextService;
+
+ private XdatUserAuthService _xdatUserAuthService;
}
diff --git a/src/main/java/org/nrg/xnat/utils/XnatUserProvider.java b/src/main/java/org/nrg/xnat/utils/XnatUserProvider.java
index 42d296ce..cbc893b8 100644
--- a/src/main/java/org/nrg/xnat/utils/XnatUserProvider.java
+++ b/src/main/java/org/nrg/xnat/utils/XnatUserProvider.java
@@ -10,13 +10,15 @@
*/
package org.nrg.xnat.utils;
-import javax.inject.Provider;
-
import org.nrg.xdat.security.helpers.Users;
import org.nrg.xft.security.UserI;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import org.springframework.stereotype.Component;
+
+import javax.inject.Provider;
+@Component
public class XnatUserProvider implements Provider<UserI> {
public XnatUserProvider(final String login) {
_login = login;
diff --git a/src/main/resources/META-INF/xnat/entities/xnat-entity-packages.txt b/src/main/resources/META-INF/xnat/entities/xnat-entity-packages.txt
new file mode 100644
index 00000000..91c8dacd
--- /dev/null
+++ b/src/main/resources/META-INF/xnat/entities/xnat-entity-packages.txt
@@ -0,0 +1,12 @@
+org.nrg.automation.entities
+org.nrg.config.entities
+org.nrg.dcm.xnat
+org.nrg.framework.datacache
+org.nrg.notify.entities
+org.nrg.prefs.entities
+org.nrg.xdat.entities
+org.nrg.xft.entities
+org.nrg.xft.event.entities
+org.nrg.xnat.entities
+org.nrg.xnat.event.entities
+org.nrg.xnat.spawner.entities
diff --git a/src/main/webapp/WEB-INF/conf/TurbineResources.properties b/src/main/webapp/WEB-INF/conf/TurbineResources.properties
index f6653832..4671c0b6 100644
--- a/src/main/webapp/WEB-INF/conf/TurbineResources.properties
+++ b/src/main/webapp/WEB-INF/conf/TurbineResources.properties
@@ -270,7 +270,7 @@ services.ServletService.classname=org.apache.turbine.services.servlet.TurbineSer
services.AssemblerBrokerService.classname=org.apache.turbine.services.assemblerbroker.TurbineAssemblerBrokerService
services.GlobalCacheService.classname=org.apache.turbine.services.cache.TurbineGlobalCacheService
services.PullService.classname=org.apache.turbine.services.pull.TurbinePullService
-services.IntakeService.classname=org.apache.turbine.services.intake.TurbineIntakeService
+# services.IntakeService.classname=org.apache.turbine.services.intake.TurbineIntakeService
services.TemplateService.classname=org.apache.turbine.services.template.TurbineTemplateService
services.VelocityService.classname=org.apache.turbine.services.velocity.TurbineVelocityService
services.UploadService.classname=org.apache.turbine.services.upload.TurbineUploadService
@@ -421,7 +421,7 @@ tool.session.sessionData=org.apache.turbine.services.pull.util.SessionData
# These are intake tools.
#tool.request.om=org.apache.turbine.om.OMTool
-tool.request.intake=org.apache.turbine.services.intake.IntakeTool
+# tool.request.intake=org.apache.turbine.services.intake.IntakeTool
# This is a tool that allows access to the scheduler service.
#tool.request.scheduler=org.apache.turbine.services.SchedulerTool
@@ -630,7 +630,7 @@ services.PoolService.pool.capacity = 128
#
# Default: WEB-INF/appData.ser
#
-services.IntakeService.serialize.path= none
+# services.IntakeService.serialize.path= none
#WEB-INF/appData.ser
#--------------------------------------------------------------------
diff --git a/src/main/webapp/WEB-INF/conf/mq-context.xml b/src/main/webapp/WEB-INF/conf/mq-context.xml
index 5e682487..2afc1210 100644
--- a/src/main/webapp/WEB-INF/conf/mq-context.xml
+++ b/src/main/webapp/WEB-INF/conf/mq-context.xml
@@ -12,17 +12,12 @@
<beans xmlns="http://www.springframework.org/schema/beans"
xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:context="http://www.springframework.org/schema/context"
xmlns:amq="http://activemq.apache.org/schema/core"
xmlns:jms="http://www.springframework.org/schema/jms"
xsi:schemaLocation="http://www.springframework.org/schema/beans http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/context http://www.springframework.org/schema/context/spring-context.xsd
http://activemq.apache.org/schema/core http://activemq.apache.org/schema/core/activemq-core.xsd
http://www.springframework.org/schema/jms http://www.springframework.org/schema/jms/spring-jms.xsd">
- <!-- Pull in property values from services definition files. -->
- <context:property-placeholder location="WEB-INF/conf/services.properties, WEB-INF/conf/services-custom.properties" ignore-resource-not-found="true" ignore-unresolvable="true" />
-
<!-- embedded ActiveMQ Broker -->
<amq:broker id="activeMQBroker" brokerName="activeMQBroker" useJmx="false" persistent="true" schedulerSupport="false" useShutdownHook="false">
<amq:persistenceAdapter>
@@ -33,9 +28,9 @@
</amq:persistenceAdapter>
<amq:systemUsage>
<amq:systemUsage>
- <amq:tempUsage><amq:tempUsage limit="${amq.usage.temp}"/></amq:tempUsage>
- <amq:memoryUsage><amq:memoryUsage limit="${amq.usage.mem}"/></amq:memoryUsage>
- <amq:storeUsage><amq:storeUsage limit="${amq.usage.store}"/></amq:storeUsage>
+ <amq:tempUsage><amq:tempUsage limit="${amq.usage.temp:128mb}"/></amq:tempUsage>
+ <amq:memoryUsage><amq:memoryUsage limit="${amq.usage.mem:512mb}"/></amq:memoryUsage>
+ <amq:storeUsage><amq:storeUsage limit="${amq.usage.store:1gb}"/></amq:storeUsage>
</amq:systemUsage>
</amq:systemUsage>
</amq:broker>
diff --git a/src/main/webapp/WEB-INF/conf/xnat-conf.properties b/src/main/webapp/WEB-INF/conf/xnat-conf.properties
index 518aba10..0592e4d2 100644
--- a/src/main/webapp/WEB-INF/conf/xnat-conf.properties
+++ b/src/main/webapp/WEB-INF/conf/xnat-conf.properties
@@ -15,4 +15,8 @@ hibernate.dialect=org.hibernate.dialect.PostgreSQL9Dialect
hibernate.hbm2ddl.auto=update
hibernate.show_sql=false
hibernate.cache.use_second_level_cache=true
-hibernate.cache.use_query_cache=true
\ No newline at end of file
+hibernate.cache.use_query_cache=true
+
+amq.usage.temp=128mb
+amq.usage.mem=512mb
+amq.usage.store=1gb
--
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