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 112eac6d6ca87b23654a7cbb923e347908751dbc..a83585802358eebeec89d4a7121751e45487f222 100644
--- a/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java
+++ b/src/main/java/org/nrg/xapi/rest/event/EventHandlerApi.java
@@ -1,8 +1,12 @@
package org.nrg.xapi.rest.event;
-import io.swagger.annotations.*;
+import com.google.common.collect.Lists;
+import io.swagger.annotations.Api;
+import io.swagger.annotations.ApiOperation;
+import io.swagger.annotations.ApiResponse;
+import io.swagger.annotations.ApiResponses;
import javassist.Modifier;
-
+import org.nrg.framework.annotations.XapiRestController;
import org.nrg.framework.utilities.Reflection;
import org.nrg.xapi.model.event.EventClassInfo;
import org.nrg.xdat.XDAT;
@@ -27,10 +31,12 @@ import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
import org.springframework.security.core.context.SecurityContextHolder;
-import org.springframework.web.bind.annotation.*;
-
-import com.google.common.collect.Lists;
+import org.springframework.web.bind.annotation.PathVariable;
+import org.springframework.web.bind.annotation.RequestMapping;
+import org.springframework.web.bind.annotation.RequestMethod;
+import org.springframework.web.bind.annotation.ResponseBody;
+import javax.annotation.PostConstruct;
import java.io.IOException;
import java.lang.annotation.Annotation;
import java.lang.reflect.Method;
@@ -39,40 +45,46 @@ import java.util.Collections;
import java.util.List;
import java.util.Map;
-import javax.annotation.PostConstruct;
-
/**
* The Class EventHandlerApi.
*/
@Api(description = "The XNAT Event Handler API")
-@RestController
+@XapiRestController
public class EventHandlerApi {
-
- /** The Constant _log. */
+
+ /**
+ * The Constant _log.
+ */
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. */
- @SuppressWarnings("MismatchedQueryAndUpdateOfCollection")
- @Autowired
+
+ /**
+ * The event ids service.
+ */
+ @Autowired
+ private HibernateAutomationEventIdsService eventIdsService;
+
+ /**
+ * The filters service.
+ */
+ @Autowired
+ private HibernateAutomationFiltersService filtersService;
+
+ /**
+ * The event packages.
+ */
+ @SuppressWarnings("MismatchedQueryAndUpdateOfCollection")
+ @Autowired
private EventPackages eventPackages;
-
+
/**
* Inits the this.
*/
@PostConstruct
private void initThis() {
- getEventIdsService();
- getFiltersService();
+ getEventIdsService();
+ getFiltersService();
}
-
+
/**
* Automation event classes get.
*
@@ -85,12 +97,12 @@ public class EventHandlerApi {
@ResponseBody
public ResponseEntity<List<EventClassInfo>> automationEventClassesGet(@PathVariable("project_id") String project_id) {
final HttpStatus status = isPermitted(project_id);
- if (status != null) {
- return new ResponseEntity<>(status);
- }
+ if (status != null) {
+ return new ResponseEntity<>(status);
+ }
return new ResponseEntity<>(getEventInfoList(project_id), HttpStatus.OK);
}
-
+
/**
* Automation event classes get.
*
@@ -102,151 +114,151 @@ public class EventHandlerApi {
@ResponseBody
public ResponseEntity<List<EventClassInfo>> automationEventClassesGet() {
final HttpStatus status = isPermitted(null);
- if (status != null) {
- return new ResponseEntity<>(status);
- }
+ if (status != null) {
+ return new ResponseEntity<>(status);
+ }
return new ResponseEntity<>(getEventInfoList(null), HttpStatus.OK);
}
- /**
- * Gets the event info list.
- *
- * @param project_id the project_id
- * @return the event info list
- */
- private List<EventClassInfo> getEventInfoList(String project_id) {
- final List<EventClassInfo> eventInfoList = Lists.newArrayList();
- final List<AutomationEventIds> eventIdsList = getEventIdsService().getEventIds(project_id, false);
- final List<AutomationFilters> filtersList = getFiltersService().getAutomationFilters(project_id, false);
- for (final String className : getEventClassList(eventIdsList)) {
- final EventClassInfo eci = new EventClassInfo(className);
- final List<String> eventIds = eci.getEventIds();
- final Map<String, List<String>> filterableFields = eci.getFilterableFieldsMap();
- if (eci.getIncludeEventIdsFromDatabase()) {
- for (final AutomationEventIds autoIds : eventIdsList) {
- if (autoIds.getSrcEventClass().equals(className)) {
- for (String eId : autoIds.getEventIds()) {
- if (!eventIds.contains(eId)) {
- eventIds.add(eId);
- }
- }
- }
- }
- }
- Collections.sort(eventIds);
- try {
- for (final Method method : Arrays.asList(Class.forName(className).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);
- final Annotation anno = AnnotationUtils.findAnnotation(method, Filterable.class);
-
- final Object annoInitialValuesObj = AnnotationUtils.getValue(anno, "initialValues");
- final String[] annoInitialValues = (annoInitialValuesObj != null && annoInitialValuesObj instanceof String[]) ? (String[])annoInitialValuesObj : new String[] {};
-
- final Object annoIncludeValuesFromDatabase = AnnotationUtils.getValue(anno, "includeValuesFromDatabase");
- boolean includeValuesFromDatabase = !(annoIncludeValuesFromDatabase != null && annoIncludeValuesFromDatabase instanceof Boolean) || (boolean) annoIncludeValuesFromDatabase;
- if (!filterableFields.containsKey(column)) {
- final List<String> newValueList = Lists.newArrayList();
- filterableFields.put(column,newValueList);
- }
- final List<String> valueList = filterableFields.get(column);
- valueList.addAll(Arrays.asList(annoInitialValues));
- if (includeValuesFromDatabase) {
- for (final AutomationFilters autoFilters : filtersList) {
- if (autoFilters.getField().equals(column)) {
- valueList.addAll(autoFilters.getValues());
- break;
- }
- }
- }
- Collections.sort(valueList);
- }
- }
- } catch (SecurityException | ClassNotFoundException e) {
- for (final AutomationFilters autoFilters : filtersList) {
- if (!filterableFields.containsKey(autoFilters.getField())) {
- final List<String> valueList = Lists.newArrayList(autoFilters.getValues());
- Collections.sort(valueList);
- filterableFields.put(autoFilters.getField(), valueList);
- } else {
- for (String value : autoFilters.getValues()) {
- final List<String> values = filterableFields.get(autoFilters.getField());
- if (!values.contains(value)) {
- values.add(value);
- }
- Collections.sort(values);
- }
- }
- }
- }
- eventInfoList.add(eci);
- }
- return eventInfoList;
- }
+ /**
+ * Gets the event info list.
+ *
+ * @param project_id the project_id
+ * @return the event info list
+ */
+ private List<EventClassInfo> getEventInfoList(String project_id) {
+ final List<EventClassInfo> eventInfoList = Lists.newArrayList();
+ final List<AutomationEventIds> eventIdsList = getEventIdsService().getEventIds(project_id, false);
+ final List<AutomationFilters> filtersList = getFiltersService().getAutomationFilters(project_id, false);
+ for (final String className : getEventClassList(eventIdsList)) {
+ final EventClassInfo eci = new EventClassInfo(className);
+ final List<String> eventIds = eci.getEventIds();
+ final Map<String, List<String>> filterableFields = eci.getFilterableFieldsMap();
+ if (eci.getIncludeEventIdsFromDatabase()) {
+ for (final AutomationEventIds autoIds : eventIdsList) {
+ if (autoIds.getSrcEventClass().equals(className)) {
+ for (String eId : autoIds.getEventIds()) {
+ if (!eventIds.contains(eId)) {
+ eventIds.add(eId);
+ }
+ }
+ }
+ }
+ }
+ Collections.sort(eventIds);
+ try {
+ for (final Method method : Arrays.asList(Class.forName(className).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);
+ final Annotation anno = AnnotationUtils.findAnnotation(method, Filterable.class);
+
+ final Object annoInitialValuesObj = AnnotationUtils.getValue(anno, "initialValues");
+ final String[] annoInitialValues = (annoInitialValuesObj != null && annoInitialValuesObj instanceof String[]) ? (String[]) annoInitialValuesObj : new String[] {};
- /**
- * Gets the event class list.
- *
- * @param eventIdsList the event ids list
- * @return the event class list
- */
- 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
- if (eventPackages != null) {
- for (final String pkg : eventPackages) {
- try {
- for (final Class<?> clazz : Reflection.getClassesForPackage(pkg)) {
- if (AutomationEventImplementerI.class.isAssignableFrom(clazz) && !clazz.isInterface() &&
- !Modifier.isAbstract(clazz.getModifiers())) {
- if (!classList.contains(clazz.getName())) {
- classList.add(clazz.getName());
- }
- }
- }
- } catch (ClassNotFoundException | IOException e) {
- // Do nothing.
- }
- }
- }
- // I think for now we'll not pull from the database if we've found event classes. If the database
- // contains any thing different, it should only be event classes that are no longer available.
- if (classList.size()<1) {
- for (final AutomationEventIds auto : eventIdsList) {
- if (!classList.contains(auto.getSrcEventClass())) {
- classList.add(auto.getSrcEventClass());
- }
- }
- }
+ final Object annoIncludeValuesFromDatabase = AnnotationUtils.getValue(anno, "includeValuesFromDatabase");
+ boolean includeValuesFromDatabase = !(annoIncludeValuesFromDatabase != null && annoIncludeValuesFromDatabase instanceof Boolean) || (boolean) annoIncludeValuesFromDatabase;
+ if (!filterableFields.containsKey(column)) {
+ final List<String> newValueList = Lists.newArrayList();
+ filterableFields.put(column, newValueList);
+ }
+ final List<String> valueList = filterableFields.get(column);
+ valueList.addAll(Arrays.asList(annoInitialValues));
+ if (includeValuesFromDatabase) {
+ for (final AutomationFilters autoFilters : filtersList) {
+ if (autoFilters.getField().equals(column)) {
+ valueList.addAll(autoFilters.getValues());
+ break;
+ }
+ }
+ }
+ Collections.sort(valueList);
+ }
+ }
+ } catch (SecurityException | ClassNotFoundException e) {
+ for (final AutomationFilters autoFilters : filtersList) {
+ if (!filterableFields.containsKey(autoFilters.getField())) {
+ final List<String> valueList = Lists.newArrayList(autoFilters.getValues());
+ Collections.sort(valueList);
+ filterableFields.put(autoFilters.getField(), valueList);
+ } else {
+ for (String value : autoFilters.getValues()) {
+ final List<String> values = filterableFields.get(autoFilters.getField());
+ if (!values.contains(value)) {
+ values.add(value);
+ }
+ Collections.sort(values);
+ }
+ }
+ }
+ }
+ eventInfoList.add(eci);
+ }
+ return eventInfoList;
+ }
+
+ /**
+ * Gets the event class list.
+ *
+ * @param eventIdsList the event ids list
+ * @return the event class list
+ */
+ 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
+ if (eventPackages != null) {
+ for (final String pkg : eventPackages) {
+ try {
+ for (final Class<?> clazz : Reflection.getClassesForPackage(pkg)) {
+ if (AutomationEventImplementerI.class.isAssignableFrom(clazz) && !clazz.isInterface() &&
+ !Modifier.isAbstract(clazz.getModifiers())) {
+ if (!classList.contains(clazz.getName())) {
+ classList.add(clazz.getName());
+ }
+ }
+ }
+ } catch (ClassNotFoundException | IOException e) {
+ // Do nothing.
+ }
+ }
+ }
+ // I think for now we'll not pull from the database if we've found event classes. If the database
+ // contains any thing different, it should only be event classes that are no longer available.
+ if (classList.size() < 1) {
+ for (final AutomationEventIds auto : eventIdsList) {
+ if (!classList.contains(auto.getSrcEventClass())) {
+ classList.add(auto.getSrcEventClass());
+ }
+ }
+ }
return classList;
- }
-
- /**
- * Gets the event ids service.
- *
- * @return the event ids service
- */
- private HibernateAutomationEventIdsService getEventIdsService() {
- if (eventIdsService == null) {
- eventIdsService = XDAT.getContextService().getBean(HibernateAutomationEventIdsService.class);
- }
- return eventIdsService;
- }
-
- /**
- * Gets the filters service.
- *
- * @return the filters service
- */
- private HibernateAutomationFiltersService getFiltersService() {
- if (filtersService == null) {
- filtersService = XDAT.getContextService().getBean(HibernateAutomationFiltersService.class);
- }
- return filtersService;
- }
-
+ }
+
+ /**
+ * Gets the event ids service.
+ *
+ * @return the event ids service
+ */
+ private HibernateAutomationEventIdsService getEventIdsService() {
+ if (eventIdsService == null) {
+ eventIdsService = XDAT.getContextService().getBean(HibernateAutomationEventIdsService.class);
+ }
+ return eventIdsService;
+ }
+
+ /**
+ * Gets the filters service.
+ *
+ * @return the filters service
+ */
+ private HibernateAutomationFiltersService getFiltersService() {
+ if (filtersService == null) {
+ filtersService = XDAT.getContextService().getBean(HibernateAutomationFiltersService.class);
+ }
+ return filtersService;
+ }
+
/**
* Gets the session user.
*
@@ -259,7 +271,7 @@ public class EventHandlerApi {
}
return null;
}
-
+
/**
* Checks if is permitted.
*
@@ -269,20 +281,19 @@ public class EventHandlerApi {
private HttpStatus isPermitted(String projectId) {
final UserI sessionUser = getSessionUser();
if ((sessionUser instanceof XDATUser)) {
- if (projectId != null) {
- final XnatProjectdata project = AutoXnatProjectdata.getXnatProjectdatasById(projectId, sessionUser, false);
- try {
- return Permissions.canEdit(sessionUser, project) ? null : HttpStatus.FORBIDDEN;
- } catch (Exception e) {
- _log.error("Error checking read status for project",e);
- return HttpStatus.INTERNAL_SERVER_ERROR;
- }
- } else {
- return (Roles.isSiteAdmin(sessionUser)) ? null : HttpStatus.FORBIDDEN;
- }
+ if (projectId != null) {
+ final XnatProjectdata project = AutoXnatProjectdata.getXnatProjectdatasById(projectId, sessionUser, false);
+ try {
+ return Permissions.canEdit(sessionUser, project) ? null : HttpStatus.FORBIDDEN;
+ } catch (Exception e) {
+ _log.error("Error checking read status for project", e);
+ return HttpStatus.INTERNAL_SERVER_ERROR;
+ }
+ } else {
+ return (Roles.isSiteAdmin(sessionUser)) ? null : HttpStatus.FORBIDDEN;
+ }
}
- _log.error("Error checking read status for project");
- return HttpStatus.INTERNAL_SERVER_ERROR;
+ _log.error("Error checking read status for project");
+ return HttpStatus.INTERNAL_SERVER_ERROR;
}
-
}
diff --git a/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java b/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
index e1c2fa71e2c71defc29ddd250daa6f5ce680356a..6c3ca05a8742c8588c6e7d9eb69496c13b95a192 100644
--- a/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
+++ b/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
@@ -22,7 +22,7 @@ import java.util.HashMap;
import java.util.List;
import java.util.Map;
-@Api(description = "XNAT Site Configuration Management API")
+@Api(description = "Site Configuration Management API")
@XapiRestController
@RequestMapping(value = "/siteConfig")
public class SiteConfigApi extends AbstractXnatRestApi {
diff --git a/src/main/java/org/nrg/xapi/rest/users/UsersApi.java b/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
index 5dec06a54ac399fd3ffed9684c53c53b23f2acdc..68728939142e621dd9ea0610e53986921f03f694 100644
--- a/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
+++ b/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
@@ -26,7 +26,7 @@ import org.springframework.web.bind.annotation.*;
import java.util.*;
-@Api(description = "The XNAT POC User Management API")
+@Api(description = "User Management API")
@XapiRestController
@RequestMapping(value = "/users")
public class UsersApi extends AbstractXnatRestApi {
@@ -44,26 +44,25 @@ public class UsersApi extends AbstractXnatRestApi {
@ApiResponses({@ApiResponse(code = 200, message = "An array of user profiles"), @ApiResponse(code = 500, message = "Unexpected error")})
@RequestMapping(value = {"/profiles"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = RequestMethod.GET)
@ResponseBody
- public ResponseEntity<List<Map<String,String>>> usersProfilesGet() {
- List<UserI> users = Users.getUsers();
- List<Map<String,String>> userMaps = new ArrayList<Map<String,String>>();
- for(UserI user : users){
- try{
- Map<String,String> userMap = new HashMap<String,String>();
- userMap.put("firstname",user.getFirstname());
- userMap.put("lastname",user.getLastname());
- userMap.put("username",user.getUsername());
- userMap.put("email",user.getEmail());
- userMap.put("id",String.valueOf(user.getID()));
- userMap.put("enabled",String.valueOf(user.isEnabled()));
- userMap.put("verified",String.valueOf(user.isVerified()));
+ public ResponseEntity<List<Map<String, String>>> usersProfilesGet() {
+ List<UserI> users = Users.getUsers();
+ List<Map<String, String>> userMaps = new ArrayList<>();
+ for (UserI user : users) {
+ try {
+ Map<String, String> userMap = new HashMap<>();
+ userMap.put("firstname", user.getFirstname());
+ userMap.put("lastname", user.getLastname());
+ userMap.put("username", user.getUsername());
+ userMap.put("email", user.getEmail());
+ userMap.put("id", String.valueOf(user.getID()));
+ userMap.put("enabled", String.valueOf(user.isEnabled()));
+ userMap.put("verified", String.valueOf(user.isVerified()));
userMaps.add(userMap);
- }
- catch(Exception e){
+ } catch (Exception e) {
_log.error("", e);
}
}
- return new ResponseEntity<List<Map<String,String>>>(userMaps, HttpStatus.OK);
+ return new ResponseEntity<>(userMaps, HttpStatus.OK);
}
@ApiOperation(value = "Gets the user with the specified user ID.", notes = "Returns the serialized user object with the specified user ID.", response = User.class)
@@ -94,13 +93,10 @@ public class UsersApi extends AbstractXnatRestApi {
if (status != null) {
return new ResponseEntity<>(status);
}
- UserI user = null;
+ UserI user;
try {
user = Users.getUser(username);
} catch (Exception e) {
- user = null;
- }
- if (user == null) {
//Create new User
user = Users.createUser();
user.setLogin(username);
@@ -114,9 +110,9 @@ public class UsersApi extends AbstractXnatRestApi {
if ((StringUtils.isNotBlank(model.getEmail())) && (!StringUtils.equals(model.getEmail(), user.getEmail()))) {
user.setEmail(model.getEmail());
}
- if (model.isEnabled()!=user.isEnabled()) {
+ if (model.isEnabled() != user.isEnabled()) {
user.setEnabled(model.isEnabled());
- if(!model.isEnabled()){
+ if (!model.isEnabled()) {
//When a user is disabled, deactivate all their AliasTokens
try {
XDAT.getContextService().getBean(AliasTokenService.class).deactivateAllTokensForUser(user.getLogin());
@@ -125,7 +121,7 @@ public class UsersApi extends AbstractXnatRestApi {
}
}
}
- if (model.isVerified()!=user.isVerified()) {
+ if (model.isVerified() != user.isVerified()) {
user.setVerified(model.isVerified());
}
@@ -253,7 +249,7 @@ public class UsersApi extends AbstractXnatRestApi {
if (user == null) {
return new ResponseEntity<>(HttpStatus.NOT_FOUND);
}
- Collection<String> roles = Roles.getRoles(user);
+ Collection<String> roles = Roles.getRoles(user);
return new ResponseEntity<>(roles, HttpStatus.OK);
} catch (UserInitException e) {
_log.error("An error occurred initializing the user " + id, e);
@@ -277,10 +273,10 @@ public class UsersApi extends AbstractXnatRestApi {
return new ResponseEntity<>(HttpStatus.NOT_FOUND);
}
try {
- Roles.addRole(getSessionUser(),user,role);
+ Roles.addRole(getSessionUser(), user, role);
return new ResponseEntity<>(HttpStatus.OK);
} catch (Exception e) {
- _log.error("Error occurred adding role "+role+" to user " + user.getLogin()+".");
+ _log.error("Error occurred adding role " + role + " to user " + user.getLogin() + ".");
}
return new ResponseEntity<>(false, HttpStatus.INTERNAL_SERVER_ERROR);
} catch (UserInitException e) {
@@ -306,10 +302,10 @@ public class UsersApi extends AbstractXnatRestApi {
return new ResponseEntity<>(HttpStatus.NOT_FOUND);
}
try {
- Roles.deleteRole(getSessionUser(),user,role);
+ Roles.deleteRole(getSessionUser(), user, role);
return new ResponseEntity<>(HttpStatus.OK);
} catch (Exception e) {
- _log.error("Error occurred removing role "+role+" from user " + user.getLogin()+".");
+ _log.error("Error occurred removing role " + role + " from user " + user.getLogin() + ".");
}
return new ResponseEntity<>(false, HttpStatus.INTERNAL_SERVER_ERROR);
} catch (UserInitException e) {
@@ -357,10 +353,10 @@ public class UsersApi extends AbstractXnatRestApi {
return new ResponseEntity<>(HttpStatus.NOT_FOUND);
}
try {
- Groups.addUserToGroup(group, user, getSessionUser(),null);
+ Groups.addUserToGroup(group, user, getSessionUser(), null);
return new ResponseEntity<>(HttpStatus.OK);
} catch (Exception e) {
- _log.error("Error occurred adding user " + user.getLogin()+ " to group "+group+".");
+ _log.error("Error occurred adding user " + user.getLogin() + " to group " + group + ".");
}
return new ResponseEntity<>(false, HttpStatus.INTERNAL_SERVER_ERROR);
} catch (UserInitException e) {
@@ -389,7 +385,7 @@ public class UsersApi extends AbstractXnatRestApi {
Groups.removeUserFromGroup(user, group, null);
return new ResponseEntity<>(HttpStatus.OK);
} catch (Exception e) {
- _log.error("Error occurred removing user "+user.getLogin()+" from group " + group+".");
+ _log.error("Error occurred removing user " + user.getLogin() + " from group " + group + ".");
}
return new ResponseEntity<>(false, HttpStatus.INTERNAL_SERVER_ERROR);
} catch (UserInitException e) {
diff --git a/src/main/java/org/nrg/xnat/configuration/WebConfig.java b/src/main/java/org/nrg/xnat/configuration/WebConfig.java
index bf51d79008c082c52f1cc775269666d324232665..b6bcb890a39819f8492dade1c4dc5573154bde16 100644
--- a/src/main/java/org/nrg/xnat/configuration/WebConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/WebConfig.java
@@ -1,9 +1,5 @@
package org.nrg.xnat.configuration;
-import com.fasterxml.jackson.annotation.JsonInclude;
-import com.fasterxml.jackson.core.JsonParser;
-import com.fasterxml.jackson.databind.SerializationFeature;
-import com.fasterxml.jackson.datatype.hibernate4.Hibernate4Module;
import org.nrg.framework.annotations.XapiRestController;
import org.nrg.xnat.spawner.configuration.SpawnerConfig;
import org.slf4j.Logger;
@@ -14,7 +10,6 @@ import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
import org.springframework.context.support.ResourceBundleMessageSource;
-import org.springframework.http.converter.json.Jackson2ObjectMapperBuilder;
import org.springframework.web.multipart.MultipartResolver;
import org.springframework.web.multipart.support.StandardServletMultipartResolver;
import org.springframework.web.servlet.ViewResolver;
@@ -36,16 +31,6 @@ import springfox.documentation.swagger2.annotations.EnableSwagger2;
@Import(SpawnerConfig.class)
@ComponentScan({"org.nrg.xapi.rest", "org.nrg.xnat.spawner.controllers"})
public class WebConfig extends WebMvcConfigurerAdapter {
- @Bean
- public Jackson2ObjectMapperBuilder objectMapperBuilder() {
- return new Jackson2ObjectMapperBuilder()
- .serializationInclusion(JsonInclude.Include.NON_NULL)
- .failOnEmptyBeans(false)
- .featuresToEnable(JsonParser.Feature.ALLOW_SINGLE_QUOTES, JsonParser.Feature.ALLOW_YAML_COMMENTS)
- .featuresToDisable(SerializationFeature.FAIL_ON_EMPTY_BEANS, SerializationFeature.WRITE_NULL_MAP_VALUES)
- .modules(new Hibernate4Module());
- }
-
@Override
public void addResourceHandlers(ResourceHandlerRegistry registry) {
registry.addResourceHandler("**/swagger-ui.html").addResourceLocations("classpath:/META-INF/resources/");
diff --git a/src/main/java/org/nrg/xnat/initialization/RootConfig.java b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
index c29194b18cc66e240773edbe058154159cb84b36..5f3a9fffdb9f9dc297503c2b4c79ca4e2b6ccede 100644
--- a/src/main/java/org/nrg/xnat/initialization/RootConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
@@ -13,13 +13,13 @@ import org.nrg.framework.datacache.SerializerRegistry;
import org.nrg.framework.exceptions.NrgServiceException;
import org.nrg.framework.services.ContextService;
import org.nrg.framework.services.SerializerService;
+import org.nrg.framework.services.YamlObjectMapper;
+import org.nrg.prefs.beans.PreferenceBeanMixIn;
import org.nrg.xdat.preferences.InitializerSiteConfiguration;
import org.nrg.xdat.preferences.SiteConfigPreferences;
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;
+import org.springframework.context.annotation.*;
+import org.springframework.http.converter.json.Jackson2ObjectMapperBuilder;
import org.springframework.http.converter.xml.MarshallingHttpMessageConverter;
import org.springframework.oxm.jaxb.Jaxb2Marshaller;
@@ -58,35 +58,34 @@ public class RootConfig {
@Bean
public PrettyPrinter prettyPrinter() {
- final DefaultIndenter indenter = new DefaultIndenter(" ", DefaultIndenter.SYS_LF);
return new DefaultPrettyPrinter() {{
+ final DefaultIndenter indenter = new DefaultIndenter(" ", DefaultIndenter.SYS_LF);
indentObjectsWith(indenter);
indentArraysWith(indenter);
}};
}
@Bean
- public ObjectMapper jsonObjectMapper() {
- final PrettyPrinter printer = prettyPrinter();
- final ObjectMapper mapper = new ObjectMapper().setDefaultPrettyPrinter(printer);
- mapper.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
- mapper.configure(SerializationFeature.FAIL_ON_EMPTY_BEANS, false);
- mapper.configure(SerializationFeature.WRITE_NULL_MAP_VALUES, false);
- mapper.configure(JsonParser.Feature.ALLOW_YAML_COMMENTS, true);
- mapper.registerModule(new Hibernate4Module());
- return mapper;
+ public Jackson2ObjectMapperBuilder objectMapperBuilder() {
+ return new Jackson2ObjectMapperBuilder()
+ .serializationInclusion(JsonInclude.Include.NON_NULL)
+ .failOnEmptyBeans(false)
+ .mixIns(mixIns())
+ .featuresToEnable(JsonParser.Feature.ALLOW_SINGLE_QUOTES, JsonParser.Feature.ALLOW_YAML_COMMENTS)
+ .featuresToDisable(SerializationFeature.FAIL_ON_EMPTY_BEANS, SerializationFeature.WRITE_NULL_MAP_VALUES)
+ .modulesToInstall(new Hibernate4Module());
}
@Bean
- public ObjectMapper yamlObjectMapper() {
- final PrettyPrinter printer = prettyPrinter();
- final ObjectMapper mapper = new ObjectMapper(new YAMLFactory()).setDefaultPrettyPrinter(printer);
- mapper.configure(JsonParser.Feature.ALLOW_SINGLE_QUOTES, true);
- mapper.configure(SerializationFeature.FAIL_ON_EMPTY_BEANS, false);
- mapper.configure(SerializationFeature.WRITE_NULL_MAP_VALUES, false);
- mapper.configure(JsonParser.Feature.ALLOW_YAML_COMMENTS, true);
- mapper.registerModule(new Hibernate4Module());
- return mapper;
+ public Map<Class<?>, Class<?>> mixIns() {
+ final Map<Class<?>, Class<?>> mixIns = new HashMap<>();
+ mixIns.put(SiteConfigPreferences.class, PreferenceBeanMixIn.class);
+ return mixIns;
+ }
+
+ @Bean
+ public YamlObjectMapper yamlObjectMapper() {
+ return new YamlObjectMapper();
}
@Bean
diff --git a/src/main/resources/log4j.properties b/src/main/resources/log4j.properties
new file mode 100644
index 0000000000000000000000000000000000000000..283396ac8ab7ea4724c69f619a146729a3cd3068
--- /dev/null
+++ b/src/main/resources/log4j.properties
@@ -0,0 +1,391 @@
+
+#
+# D:/Development/XNAT/1.6/xnat_builder_1_6dev/plugin-resources/originals/log4j.properties
+# XNAT http://www.xnat.org
+# Copyright (c) 2014, Washington University School of Medicine
+# All Rights Reserved
+#
+# Released under the Simplified BSD.
+#
+# Last modified 2/7/14 12:19 PM
+#
+
+log4j.rootLogger=ERROR, app
+
+#
+# Turbine goes into Turbine Log
+#
+log4j.category.org.apache.turbine=ERROR, turbine
+log4j.additivity.org.apache.turbine=false
+
+#
+# Velocity Logfile
+#
+log4j.category.velocity=ERROR, velocity
+log4j.additivity.velocity=false
+
+#
+# Scheduler Category
+#
+log4j.category.scheduler=ERROR, scheduler
+log4j.additivity.scheduler=false
+
+#
+# Avalon Logfile
+#
+log4j.category.avalon=ERROR, avalon
+log4j.additivity.avalon=false
+
+#
+# Axis Logfile
+#
+log4j.category.org.apache.axis=ERROR, axis
+log4j.additivity.org.apache.axis=false
+
+#
+# Application debugging
+#
+log4j.category.org.xnat.xnatfs=ERROR, xnatfs
+log4j.additivity.org.xnat.xnatfs=false
+
+#
+# Application debugging
+#
+log4j.category.org.apache.turbine.app.xnat17=ERROR, app
+log4j.additivity.org.apache.turbine.app.xnat17=false
+
+#
+# Application debugging
+#
+log4j.category.org.nrg.xdat=ERROR, xdat
+log4j.additivity.org.nrg.xdat=false
+
+#
+# Application debugging
+#
+log4j.category.org.nrg.xft=ERROR, xdat
+log4j.additivity.org.nrg.xft=false
+
+log4j.category.org.nrg.xnat=ERROR, xdat
+log4j.additivity.org.nrg.xnat=false
+
+log4j.category.org.nrg.xnat.restlet=WARN, restlet
+log4j.additivity.org.nrg.xnat.restlet=false
+
+log4j.category.org.nrg.xnat.remote=WARN, remote
+log4j.additivity.org.nrg.xnat.remote=false
+
+log4j.category.org.nrg.xnat.helpers.prearchive=WARN, prearchive
+log4j.additivity.org.nrg.xnat.helpers.prearchive=false
+
+# SETTING AccessLogger Log to INFO will log all site access
+log4j.category.org.nrg.xdat.turbine.utils.AccessLogger=INFO, access
+log4j.additivity.org.nrg.xdat.turbine.utils.AccessLogger=false
+
+# SETTING PoolDBUtils Log to DEBUG will log all SQL QUERIES
+log4j.category.org.nrg.xft.db.PoolDBUtils=ERROR, sql
+log4j.additivity.org.nrg.xft.db.PoolDBUtils=false
+
+# Analytics category, default analytics level is trace.
+# log4j.category.analytics = TRACE, analytics
+# log4j.additivity.analytics = false
+
+# Security logs, both Spring Framework and XNAT
+log4j.category.org.springframework.security=WARN, security
+log4j.additivity.org.springframework.security=false
+log4j.category.org.springframework.ldap=WARN, security
+log4j.additivity.org.springframework.ldap=false
+log4j.category.org.nrg.xnat.security=WARN, security
+log4j.additivity.org.nrg.xnat.security=false
+
+# Spring Framework logs
+log4j.category.org.springframework.beans=WARN, spring
+log4j.additivity.org.springframework.beans=false
+log4j.category.org.springframework.context=WARN, spring
+log4j.additivity.org.springframework.context=false
+log4j.category.org.springframework.core=WARN, spring
+log4j.additivity.org.springframework.core=false
+log4j.category.org.springframework.http=WARN, spring
+log4j.additivity.org.springframework.http=false
+log4j.category.org.springframework.mail=WARN, spring
+log4j.additivity.org.springframework.mail=false
+log4j.category.org.springframework.oxm=WARN, spring
+log4j.additivity.org.springframework.oxm=false
+log4j.category.org.springframework.scheduling=WARN, spring
+log4j.additivity.org.springframework.scheduling=false
+log4j.category.org.springframework.stereotype=WARN, spring
+log4j.additivity.org.springframework.stereotype=false
+log4j.category.org.springframework.util=WARN, spring
+log4j.additivity.org.springframework.util=false
+log4j.category.org.springframework.web=WARN, spring
+log4j.additivity.org.springframework.web=false
+
+# Database and ORM logging.
+log4j.category.org.nrg.framework.orm=WARN, orm
+log4j.additivity.org.nrg.framework.orm=false
+log4j.category.org.springframework.orm=WARN, orm
+log4j.additivity.org.springframework.orm=false
+log4j.category.org.springframework.dao=WARN, orm
+log4j.additivity.org.springframework.dao=false
+log4j.category.org.springframework.jdbc=WARN, orm
+log4j.additivity.org.springframework.jdbc=false
+log4j.category.org.springframework.transaction=WARN, orm
+log4j.additivity.org.springframework.transaction=false
+
+
+# DICOM services
+log4j.category.org.nrg.dcm=WARN, dicom
+log4j.additivity.org.nrg.dcm=false
+
+#
+# Automation logging
+#
+log4j.category.org.nrg.automation=ERROR, automation
+log4j.additivity.org.nrg.automation=false
+
+########################################################################
+#
+# Logfile definitions
+#
+########################################################################
+
+#
+# turbine.log
+#
+log4j.appender.turbine=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.turbine.DatePattern='.'yyy-MM-dd
+log4j.appender.turbine.file=${xnat.home}/logs/turbine.log
+log4j.appender.turbine.layout=org.apache.log4j.PatternLayout
+log4j.appender.turbine.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.turbine.append=false
+
+#
+# Scheduler Output
+#
+log4j.appender.scheduler=org.apache.log4j.FileAppender
+log4j.appender.scheduler.file=${xnat.home}/logs/scheduler.log
+log4j.appender.scheduler.layout=org.apache.log4j.PatternLayout
+log4j.appender.scheduler.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.scheduler.append=false
+
+#
+# Velocity gets configured to write its output onto the velocity
+# category.
+#
+log4j.appender.velocity=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.velocity.DatePattern='.'yyy-MM-dd
+log4j.appender.velocity.file=${xnat.home}/logs/velocity.log
+log4j.appender.velocity.layout=org.apache.log4j.PatternLayout
+log4j.appender.velocity.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.velocity.append=false
+
+#
+# Avalon gets configured to write its output onto the avalon
+# category.
+#
+log4j.appender.avalon=org.apache.log4j.FileAppender
+log4j.appender.avalon.file=${xnat.home}/logs/avalon.log
+log4j.appender.avalon.layout=org.apache.log4j.PatternLayout
+log4j.appender.avalon.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.avalon.append=false
+
+#
+# xnatfs.log
+#
+log4j.appender.xnatfs=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.xnatfs.DatePattern='.'yyy-MM-dd
+log4j.appender.xnatfs.file=${xnat.home}/logs/xnatfs.log
+log4j.appender.xnatfs.layout=org.apache.log4j.PatternLayout
+log4j.appender.xnatfs.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.xnatfs.append=false
+
+#
+# Application.log
+#
+log4j.appender.app=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.app.DatePattern='.'yyy-MM-dd
+log4j.appender.app.file=${xnat.home}/logs/application.log
+log4j.appender.app.layout=org.apache.log4j.PatternLayout
+log4j.appender.app.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.app.append=false
+
+#
+# Application.log
+#
+
+log4j.appender.axis=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.axis.DatePattern='.'yyy-MM-dd
+log4j.appender.axis.File=${xnat.home}/logs/axis.log
+log4j.appender.axis.Append=true
+log4j.appender.axis.Threshold=WARN
+log4j.appender.axis.layout=org.apache.log4j.PatternLayout
+log4j.appender.axis.layout.ConversionPattern=%-4r [%t] %-5p %c %x - %m%n
+
+#
+# XDAT
+#
+log4j.appender.xdat=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.xdat.DatePattern='.'yyy-MM-dd
+log4j.appender.xdat.file=${xnat.home}/logs/xdat.log
+log4j.appender.xdat.layout=org.apache.log4j.PatternLayout
+log4j.appender.xdat.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.xdat.append=true
+
+#
+# Restlets
+#
+log4j.appender.restlet=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.restlet.DatePattern='.'yyy-MM-dd
+log4j.appender.restlet.file=${xnat.home}/logs/restlet.log
+log4j.appender.restlet.layout=org.apache.log4j.PatternLayout
+log4j.appender.restlet.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.restlet.append=true
+
+#
+# Prearchive
+#
+log4j.appender.prearchive=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.prearchive.DatePattern='.'yyy-MM-dd
+log4j.appender.prearchive.file=${xnat.home}/logs/prearchive.log
+log4j.appender.prearchive.layout=org.apache.log4j.PatternLayout
+log4j.appender.prearchive.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.prearchive.append=true
+
+#
+# DICOM
+#
+log4j.appender.dicom=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.dicom.DatePattern='.'yyy-MM-dd
+log4j.appender.dicom.file=${xnat.home}/logs/dicom.log
+log4j.appender.dicom.layout=org.apache.log4j.PatternLayout
+log4j.appender.dicom.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.dicom.append=true
+
+#
+# ACCESS LOG
+#
+log4j.appender.access=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.access.DatePattern='.'yyy-MM-dd
+log4j.appender.access.file=${xnat.home}/logs/access.log
+log4j.appender.access.ImmediateFlush=true
+log4j.appender.access.Threshold=ERROR
+log4j.appender.access.append=true
+log4j.appender.access.layout=org.apache.log4j.PatternLayout
+log4j.appender.access.layout.conversionPattern=%d - %m%n
+
+#
+# QUERY LOG
+#
+log4j.appender.sql=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.sql.file=${xnat.home}/logs/sql.log
+log4j.appender.sql.ImmediateFlush=true
+log4j.appender.sql.DatePattern='.'yyy-MM-dd
+log4j.appender.sql.append=true
+log4j.appender.sql.layout=org.apache.log4j.PatternLayout
+log4j.appender.sql.layout.conversionPattern=%d - %m%n
+
+# REMOTE LOG
+#
+log4j.appender.remote=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.remote.file=${xnat.home}/logs/remote.log
+log4j.appender.remote.ImmediateFlush=true
+log4j.appender.remote.DatePattern='.'yyy-MM-dd
+log4j.appender.remote.append=true
+log4j.appender.remote.layout=org.apache.log4j.PatternLayout
+log4j.appender.remote.layout.conversionPattern=%d - %m%n
+
+#
+# ANALYTICS LOG
+#
+# log4j.appender.analytics = org.apache.log4j.jdbc.JDBCAppender
+# log4j.appender.analytics.layout = org.apache.log4j.PatternLayout
+# log4j.appender.analytics.layout.conversionPattern = INSERT INTO analytics (entry_date, entry_level, entry_location, message) VALUES ( '%d{yyyy-MM-dd HH:mm:ss.SSS}','%p', '%C;%L', E'%m' )
+# log4j.appender.analytics.URL = jdbc:postgresql://localhost/xnat
+# log4j.appender.analytics.Driver = org.postgresql.Driver
+# log4j.appender.analytics.User = xnat
+# log4j.appender.analytics.Password = xnat
+
+#
+# XDAT Security
+#
+log4j.appender.security=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.security.DatePattern='.'yyy-MM-dd
+log4j.appender.security.file=${xnat.home}/logs/security.log
+log4j.appender.security.layout=org.apache.log4j.PatternLayout
+log4j.appender.security.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.security.append=true
+
+#
+# Spring Framework logs
+#
+log4j.appender.spring=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.spring.DatePattern='.'yyy-MM-dd
+log4j.appender.spring.file=${xnat.home}/logs/spring.log
+log4j.appender.spring.layout=org.apache.log4j.PatternLayout
+log4j.appender.spring.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.spring.append=true
+
+#
+# NRG and Spring ORM Framework logs
+#
+log4j.appender.orm=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.orm.DatePattern='.'yyy-MM-dd
+log4j.appender.orm.file=${xnat.home}/logs/orm.log
+log4j.appender.orm.layout=org.apache.log4j.PatternLayout
+log4j.appender.orm.layout.conversionPattern=%d [%t] %-5p %c - %m%n
+log4j.appender.orm.append=true
+
+#
+# Automation log output
+#
+log4j.appender.automation=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.automation.File=${xnat.home}/logs/automation.log
+log4j.appender.automation.DatePattern='.'yyyy-MM-dd
+log4j.appender.automation.layout=org.apache.log4j.PatternLayout
+log4j.appender.automation.layout.ConversionPattern=%d %m%n
+
+#
+# Received file log
+#
+log4j.appender.RECEIVED=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.RECEIVED.File=${xnat.home}/logs/received.log
+log4j.appender.RECEIVED.DatePattern='.'yyyy-MM-dd
+log4j.appender.RECEIVED.layout=org.apache.log4j.PatternLayout
+log4j.appender.RECEIVED.layout.ConversionPattern=%d %m%n
+log4j.additivity.org.nrg.xnat.received=false
+log4j.logger.org.nrg.xnat.received=INFO,RECEIVED
+
+#
+# Pipeline Logfile
+#
+log4j.category.org.nrg.pipeline=ERROR, pipeline
+log4j.additivity.org.nrg.pipeline=false
+log4j.appender.pipeline=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.pipeline.File=${xnat.home}/logs/pipeline.log
+log4j.appender.pipeline.DatePattern='.'yyyy-MM-dd
+log4j.appender.pipeline.layout=org.apache.log4j.PatternLayout
+log4j.appender.pipeline.layout.ConversionPattern=%d %m%n
+
+#
+# Pipeline Launch Logfile
+#
+log4j.category.org.nrg.pipeline.launch=INFO, launch
+log4j.additivity.org.nrg.pipeline.launch=false
+log4j.appender.launch=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.launch.File=${xnat.home}/logs/launch.log
+log4j.appender.launch.DatePattern='.'yyyy-MM-dd
+log4j.appender.launch.layout=org.apache.log4j.PatternLayout
+log4j.appender.launch.layout.ConversionPattern=%d %m%n
+
+#
+# JMS logging
+#
+log4j.category.org.springframework.jms=INFO, jms
+log4j.additivity.org.springframework.jms=false
+log4j.category.org.nrg.xnat.services.messaging=INFO, jms
+log4j.additivity.org.nrg.xnat.services.messaging=false
+log4j.appender.jms=org.apache.log4j.DailyRollingFileAppender
+log4j.appender.jms.File=${xnat.home}/logs/jms.log
+log4j.appender.jms.DatePattern='.'yyyy-MM-dd
+log4j.appender.jms.layout=org.apache.log4j.PatternLayout
+log4j.appender.jms.layout.ConversionPattern=%d %m%n
diff --git a/src/main/webapp/WEB-INF/conf/TurbineResources.properties b/src/main/webapp/WEB-INF/conf/TurbineResources.properties
index 4671c0b610896ace9b4ca3eb1fecad9cdb80970a..84f1203ee9f171dd6e7a09736afa1807d6e2ba7c 100644
--- a/src/main/webapp/WEB-INF/conf/TurbineResources.properties
+++ b/src/main/webapp/WEB-INF/conf/TurbineResources.properties
@@ -14,7 +14,7 @@
#
# -------------------------------------------------------------------
-log4j.file = WEB-INF/conf/log4j.properties
+log4j.file =
# -------------------------------------------------------------------
#
@@ -84,7 +84,7 @@ scheduledjob.cache.size=10
# Default: org.apache.turbine.modules
# -------------------------------------------------------------------
-module.packages = org.apache.turbine.app.xnat17.modules,org.nrg.xnat.turbine.modules,org.nrg.xdat.turbine.modules
+module.packages = org.apache.turbine.app.xnat.modules,org.nrg.xnat.turbine.modules,org.nrg.xdat.turbine.modules
# -------------------------------------------------------------------
#