XNAT-4346 XNAT-4330 Changed AbstractXnatRestApi to AbstractXapiRestController....

XNAT-4346 XNAT-4330 Changed AbstractXnatRestApi to AbstractXapiRestController. Fixed logic in permissions check that broke certain saved searches.

build.gradle

@@ -385,9 +385,10 @@ dependencies {
     compile "org.apache.httpcomponents:httpcore-nio:4.4.4"
 
     compile "org.codehaus.groovy:groovy-all:${vGroovy}"
-    compile "org.python:jython-standalone:${vJython}"
+    compile "org.python:jython:${vJython}"
 
     compile "net.sourceforge.saxon:saxon:${vSaxon}"
+    compile "xalan:xalan:2.7.2"
 
     compile "nl.bitwalker:UserAgentUtils:1.2.4"
     compile "com.twmacinta:fast-md5:2.7.1"
@@ -423,7 +424,6 @@ dependencies {
     runtime "net.imagej:ij:1.50e"
     runtime "net.bull.javamelody:javamelody-core:1.58.0"
     runtime "org.javassist:javassist:3.20.0-GA"
-    runtime "xalan:xalan:2.7.2"
 
     providedCompile "javax.servlet:javax.servlet-api:${vServletApi}"
 

gradle/wrapper/gradle-wrapper.properties

-#Sat May 28 14:49:32 CDT 2016
+#Thu Jul 07 14:39:27 CDT 2016
 distributionBase=GRADLE_USER_HOME
 distributionPath=wrapper/dists
 zipStoreBase=GRADLE_USER_HOME
 zipStorePath=wrapper/dists
-distributionUrl=https\://services.gradle.org/distributions/gradle-2.13-bin.zip
+distributionUrl=https\://services.gradle.org/distributions/gradle-2.13-all.zip

src/main/java/org/nrg/xapi/rest/dicomscp/DicomSCPApi.java

@@ -6,7 +6,7 @@ import org.nrg.dcm.preferences.DicomSCPInstance;
 import org.nrg.framework.annotations.XapiRestController;
 import org.nrg.framework.exceptions.NrgServiceException;
 import org.nrg.xapi.rest.NotFoundException;
-import org.nrg.xdat.rest.AbstractXnatRestApi;
+import org.nrg.xdat.rest.AbstractXapiRestController;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.http.HttpStatus;
@@ -20,7 +20,7 @@ import java.util.List;
 @Api(description = "XNAT DICOM SCP management API")
 @XapiRestController
 @RequestMapping(value = "/dicomscp")
-public class DicomSCPApi extends AbstractXnatRestApi {
+public class DicomSCPApi extends AbstractXapiRestController {
     private static final Logger _log = LoggerFactory.getLogger(DicomSCPApi.class);
 
     @ApiOperation(value = "Get list of all configured DICOM SCP receiver definitions.", notes = "The primary DICOM SCP retrieval function returns a list of all DICOM SCP receivers defined for the current system.", response = DicomSCPInstance.class, responseContainer = "List")

src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java

@@ -9,7 +9,7 @@ import org.nrg.notify.services.NotificationService;
 import org.nrg.prefs.exceptions.InvalidPreferenceName;
 import org.nrg.xapi.exceptions.InitializationException;
 import org.nrg.xdat.preferences.NotificationsPreferences;
-import org.nrg.xdat.rest.AbstractXnatRestApi;
+import org.nrg.xdat.rest.AbstractXapiRestController;
 import org.nrg.xnat.services.XnatAppInfo;
 import org.nrg.xnat.utils.XnatHttpUtils;
 import org.slf4j.Logger;
@@ -29,7 +29,7 @@ import java.util.*;
 @Api(description = "XNAT Notifications management API")
 @XapiRestController
 @RequestMapping(value = "/notifications")
-public class NotificationsApi extends AbstractXnatRestApi {
+public class NotificationsApi extends AbstractXapiRestController {
 
     public static final String POST_PROPERTIES_NOTES = "Sets the mail service host, port, username, password, and protocol. You can set "
                                                        + "extra properties on the mail sender (e.g. for configuring SSL or TLS transport) by "

src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java

@@ -7,7 +7,7 @@ import org.nrg.framework.annotations.XapiRestController;
 import org.nrg.prefs.exceptions.InvalidPreferenceName;
 import org.nrg.xapi.exceptions.InitializationException;
 import org.nrg.xdat.preferences.SiteConfigPreferences;
-import org.nrg.xdat.rest.AbstractXnatRestApi;
+import org.nrg.xdat.rest.AbstractXapiRestController;
 import org.nrg.xnat.services.XnatAppInfo;
 import org.nrg.xnat.turbine.utils.ArcSpecManager;
 import org.nrg.xnat.utils.XnatHttpUtils;
@@ -32,7 +32,7 @@ import java.util.Properties;
 @Api(description = "Site Configuration Management API")
 @XapiRestController
 @RequestMapping(value = "/siteConfig")
-public class SiteConfigApi extends AbstractXnatRestApi {
+public class SiteConfigApi extends AbstractXapiRestController {
     @ApiOperation(value = "Returns a map of application build properties.", notes = "This includes the implementation version, Git commit hash, and build number and number.", response = Properties.class)
     @ApiResponses({@ApiResponse(code = 200, message = "Application build properties successfully retrieved."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 500, message = "Unexpected error")})
     @RequestMapping(value = "buildInfo", produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})

src/main/java/org/nrg/xapi/rest/users/UsersApi.java

@@ -7,7 +7,7 @@ import org.nrg.xapi.model.users.User;
 import org.nrg.xapi.rest.NotFoundException;
 import org.nrg.xdat.XDAT;
 import org.nrg.xdat.preferences.SiteConfigPreferences;
-import org.nrg.xdat.rest.AbstractXnatRestApi;
+import org.nrg.xdat.rest.AbstractXapiRestController;
 import org.nrg.xdat.security.UserGroupI;
 import org.nrg.xdat.security.helpers.Groups;
 import org.nrg.xdat.security.helpers.Users;
@@ -32,7 +32,7 @@ import java.util.*;
 @Api(description = "User Management API")
 @XapiRestController
 @RequestMapping(value = "/users")
-public class UsersApi extends AbstractXnatRestApi {
+public class UsersApi extends AbstractXapiRestController {
     private static final Logger _log = LoggerFactory.getLogger(UsersApi.class);
 
     @ApiOperation(value = "Get list of users.", notes = "The primary users function returns a list of all users of the XNAT system.", response = User.class, responseContainer = "List")