From 3d64b757915533f808dfc26747a324b43dcb7b6e Mon Sep 17 00:00:00 2001
From: Rick Herrick <jrherrick@wustl.edu>
Date: Tue, 6 Sep 2016 13:07:54 -0500
Subject: [PATCH] XNAT-4301 XNAT-4394 XNAT-4500 Added @XnatMixIn class mapping
processing to RootConfig. Cleaned up User class to ignore properties we don't
want to see. Adjusted ResultSet processing to fix investigator API error.
---
build.gradle | 2 +-
.../java/org/nrg/xapi/model/users/User.java | 57 +--------
.../org/nrg/xapi/rest/data/Investigator.java | 24 ++--
.../rest/notifications/NotificationsApi.java | 5 +-
.../org/nrg/xapi/rest/users/UsersApi.java | 108 +++++++++++++-----
.../xnat/configuration/AutomationConfig.java | 6 +-
.../org/nrg/xnat/configuration/OrmConfig.java | 2 +-
.../listeners/PipelineEmailHandlerAbst.java | 2 +-
.../xnat/initialization/DatabaseConfig.java | 2 +-
.../nrg/xnat/initialization/RootConfig.java | 16 ++-
.../xnat/initialization/SecurityConfig.java | 8 +-
.../initialization/XnatWebAppInitializer.java | 2 +-
.../resources/ProjectUserListResource.java | 5 +-
.../resources/RestMockCallMapRestlet.java | 7 +-
.../restlet/resources/SecureResource.java | 4 +-
15 files changed, 126 insertions(+), 124 deletions(-)
diff --git a/build.gradle b/build.gradle
index 808fae3f..173b0b42 100644
--- a/build.gradle
+++ b/build.gradle
@@ -11,7 +11,7 @@ def vPostgreSQL = '9.4.1209.jre7'
def vServletApi = '3.1.0'
def vTomcat = '7.0.68'
def vCargo = '1.4.18'
-def vSlf4j = '1.7.15'
+def vSlf4j = '1.7.21'
def vLog4j = '1.2.17'
def vJunit = '4.12'
// def vSaxon = '9.7.0-7'
diff --git a/src/main/java/org/nrg/xapi/model/users/User.java b/src/main/java/org/nrg/xapi/model/users/User.java
index 1e88b433..53d039c0 100644
--- a/src/main/java/org/nrg/xapi/model/users/User.java
+++ b/src/main/java/org/nrg/xapi/model/users/User.java
@@ -1,7 +1,6 @@
package org.nrg.xapi.model.users;
-import com.fasterxml.jackson.annotation.JsonIgnore;
-import com.fasterxml.jackson.annotation.JsonProperty;
+import com.fasterxml.jackson.annotation.JsonIgnoreProperties;
import io.swagger.annotations.ApiModel;
import io.swagger.annotations.ApiModelProperty;
import org.apache.commons.lang3.StringUtils;
@@ -13,6 +12,7 @@ import org.nrg.xft.security.UserI;
import java.util.Date;
@ApiModel(description = "Contains the properties that define a user on the system.")
+@JsonIgnoreProperties(value = {"FullName", "Password", "Salt", "XdatUser"}, ignoreUnknown = true)
public class User {
public User() {
}
@@ -45,7 +45,6 @@ public class User {
* The user's unique key.
**/
@ApiModelProperty(value = "The user's unique key.")
- @JsonProperty("id")
public Integer getId() {
return _id;
}
@@ -58,7 +57,6 @@ public class User {
* The user's login name.
**/
@ApiModelProperty(value = "The user's login name.")
- @JsonProperty("username")
public String getUsername() {
return _username;
}
@@ -71,7 +69,6 @@ public class User {
* The user's first name.
**/
@ApiModelProperty(value = "The user's first name.")
- @JsonProperty("firstName")
public String getFirstName() {
return _firstName;
}
@@ -85,7 +82,6 @@ public class User {
* The user's last name.
**/
@ApiModelProperty(value = "The user's last name.")
- @JsonProperty("lastName")
public String getLastName() {
return _lastName;
}
@@ -99,7 +95,6 @@ public class User {
* The user's _email address.
**/
@ApiModelProperty(value = "The user's email address.")
- @JsonProperty("email")
public String getEmail() {
return _email;
}
@@ -112,7 +107,6 @@ public class User {
* Whether the user is a site administrator.
**/
@ApiModelProperty(value = "Whether the user is a site administrator.")
- @JsonProperty("admin")
public boolean isAdmin() {
return _isAdmin;
}
@@ -125,7 +119,6 @@ public class User {
* Whether the user is enabled.
**/
@ApiModelProperty(value = "Whether the user is enabled.")
- @JsonProperty("enabled")
public boolean isEnabled() {
return _isEnabled;
}
@@ -138,7 +131,6 @@ public class User {
* Whether the user is verified.
**/
@ApiModelProperty(value = "Whether the user is verified.")
- @JsonProperty("verified")
public boolean isVerified() {
return _isVerified;
}
@@ -148,24 +140,9 @@ public class User {
}
/**
- * The user's primary database (deprecated).
- **/
- @ApiModelProperty(value = "The user's primary database (deprecated).")
- @JsonProperty("dbName")
- public String getDbName() {
- return _dbName;
- }
-
- @SuppressWarnings("unused")
- public void setDbName(String dbName) {
- _dbName = dbName;
- }
-
- /**
- * The user's encrypted _password.
+ * The user's encrypted password.
**/
@ApiModelProperty(value = "The user's encrypted password.")
- @JsonProperty("password")
public String getPassword() {
return _password;
}
@@ -178,7 +155,6 @@ public class User {
* The _salt used to encrypt the user's _password.
**/
@ApiModelProperty(value = "The salt used to encrypt the user's password.")
- @JsonProperty("salt")
public String getSalt() {
return _salt;
}
@@ -192,7 +168,6 @@ public class User {
* The date and time the user record was last modified.
**/
@ApiModelProperty(value = "The date and time the user record was last modified.")
- @JsonProperty("lastModified")
public Date getLastModified() {
return _lastModified;
}
@@ -205,7 +180,6 @@ public class User {
* The user's authorization record used when logging in.
**/
@ApiModelProperty(value = "The user's authorization record used when logging in.")
- @JsonProperty("authorization")
public UserAuth getAuthorization() {
return _authorization;
}
@@ -215,34 +189,11 @@ public class User {
_authorization = authorization;
}
- @JsonIgnore
+ @ApiModelProperty(value = "The user's full name.")
public String getFullName() {
return String.format("%s %s", getFirstName(), getLastName());
}
- @JsonIgnore
- public XdatUser getXDATUser(final UserI requester) {
- final XdatUser user;
- if (StringUtils.isNotBlank(_username)) {
- user = XDATUser.getXdatUsersByLogin(_username, requester, true);
- } else if (_id != null) {
- user = AutoXdatUser.getXdatUsersByXdatUserId(_id, requester, true);
- } else {
- user = null;
- }
- if (user != null) {
- return user;
- }
- final XDATUser newUser = new XDATUser();
- newUser.setLogin(_username);
- newUser.setFirstname(_firstName);
- newUser.setLastname(_lastName);
- newUser.setEmail(_email);
- newUser.setPrimaryPassword(_password);
- newUser.setSalt(_salt);
- return newUser;
- }
-
@Override
public String toString() {
diff --git a/src/main/java/org/nrg/xapi/rest/data/Investigator.java b/src/main/java/org/nrg/xapi/rest/data/Investigator.java
index 1a9ca3ac..aa0d4792 100644
--- a/src/main/java/org/nrg/xapi/rest/data/Investigator.java
+++ b/src/main/java/org/nrg/xapi/rest/data/Investigator.java
@@ -34,15 +34,15 @@ public class Investigator implements XnatInvestigatordataI {
}
public Investigator(final ResultSet resultSet) throws SQLException {
- _xnatInvestigatordataId = resultSet.getInt(0);
- _id = resultSet.getString(1);
- _title = resultSet.getString(2);
- _firstname = resultSet.getString(2);
- _lastname = resultSet.getString(2);
- _institution = resultSet.getString(2);
- _department = resultSet.getString(2);
- _email = resultSet.getString(2);
- _phone = resultSet.getString(2);
+ _xnatInvestigatordataId = resultSet.getInt(1);
+ _id = resultSet.getString(2);
+ _title = resultSet.getString(3);
+ _firstname = resultSet.getString(4);
+ _lastname = resultSet.getString(5);
+ _institution = resultSet.getString(6);
+ _department = resultSet.getString(7);
+ _email = resultSet.getString(8);
+ _phone = resultSet.getString(9);
_primaryProjects.addAll(getProjectIds(resultSet.getArray(10)));
_investigatorProjects.addAll(getProjectIds(resultSet.getArray(11)));
}
@@ -192,7 +192,11 @@ public class Investigator implements XnatInvestigatordataI {
if (array == null) {
return Collections.emptyList();
}
- return Arrays.asList((String[]) array.getArray());
+ final String[] projectIds = (String[]) array.getArray();
+ if (projectIds.length == 0) {
+ return Collections.emptyList();
+ }
+ return Arrays.asList(projectIds);
}
private final Integer _xnatInvestigatordataId;
diff --git a/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java b/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java
index e9a01c25..0d569362 100644
--- a/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java
+++ b/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java
@@ -1,6 +1,5 @@
package org.nrg.xapi.rest.notifications;
-import com.fasterxml.jackson.core.type.TypeReference;
import io.swagger.annotations.*;
import org.apache.commons.lang3.StringUtils;
import org.nrg.framework.annotations.XapiRestController;
@@ -26,7 +25,6 @@ import org.springframework.web.bind.annotation.*;
import javax.inject.Inject;
import javax.servlet.http.HttpServletRequest;
import java.io.IOException;
-import java.util.HashMap;
import java.util.Map;
import java.util.Properties;
@@ -117,7 +115,7 @@ public class NotificationsApi extends AbstractXapiRestController {
} else if (StringUtils.equals(name, "emailRecipientUpdate")) {
_notificationsPrefs.setEmailRecipientUpdate(properties.getProperty(name));
} else if (StringUtils.equals(name, "smtpServer")) {
- _notificationsPrefs.setSmtpServer(_serializer.deserializeJson(properties.getProperty(name), TYPE_REF_HASHMAP_STRING_STRING));
+ _notificationsPrefs.setSmtpServer(_serializer.deserializeJson(properties.getProperty(name), SerializerService.TYPE_REF_MAP_STRING_STRING));
} else {
_notificationsPrefs.set(properties.getProperty(name), name);
}
@@ -829,7 +827,6 @@ public class NotificationsApi extends AbstractXapiRestController {
private static final Logger _log = LoggerFactory.getLogger(NotificationsApi.class);
private static final String NOT_SET = "NotSet";
- private final static TypeReference<HashMap<String, String>> TYPE_REF_HASHMAP_STRING_STRING = new TypeReference<HashMap<String, String>>() {};
private final NotificationsPreferences _notificationsPrefs;
private final JavaMailSenderImpl _javaMailSender;
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 af585d8c..e2d6628a 100644
--- a/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
+++ b/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
@@ -41,8 +41,11 @@ public class UsersApi extends AbstractXapiRestController {
_preferences = preferences;
}
- @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")
- @ApiResponses({@ApiResponse(code = 200, message = "An array of users"), @ApiResponse(code = 500, message = "Unexpected error")})
+ @ApiOperation(value = "Get list of users.", notes = "The primary users function returns a list of all users of the XNAT system. This includes just the username and nothing else. You can retrieve a particular user by adding the username to the REST API URL or a list of users with abbreviated user profiles by calling /xapi/users/profiles.", response = String.class, responseContainer = "List")
+ @ApiResponses({@ApiResponse(code = 200, message = "A list of usernames."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "You do not have sufficient permissions to access the list of usernames."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
@RequestMapping(produces = {MediaType.APPLICATION_JSON_VALUE}, method = RequestMethod.GET)
@ResponseBody
public ResponseEntity<List<String>> usersGet() {
@@ -56,7 +59,10 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Get list of user profiles.", notes = "The users' profiles function returns a list of all users of the XNAT system with brief information about each.", response = User.class, responseContainer = "List")
- @ApiResponses({@ApiResponse(code = 200, message = "An array of user profiles"), @ApiResponse(code = 500, message = "Unexpected error")})
+ @ApiResponses({@ApiResponse(code = 200, message = "A list of user profiles."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "You do not have sufficient permissions to access the list of usernames."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
@RequestMapping(value = {"profiles"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = RequestMethod.GET)
@ResponseBody
public ResponseEntity<List<Map<String, String>>> usersProfilesGet() {
@@ -90,8 +96,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Gets the user with the specified user ID.", notes = "Returns the serialized user object with the specified user ID.", response = User.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User successfully retrieved."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to view this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
+ @ApiResponses({@ApiResponse(code = 200, message = "User successfully retrieved."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to view this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
public ResponseEntity<User> usersIdGet(@ApiParam(value = "ID of the user to fetch", required = true) @PathVariable("id") String id) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -110,8 +120,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Creates or updates the user object with the specified username.", notes = "Returns the updated serialized user object with the specified username.", response = User.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User successfully created or updated."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to create or update this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
+ @ApiResponses({@ApiResponse(code = 200, message = "User successfully created or updated."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to create or update this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
public ResponseEntity<User> usersIdPut(@ApiParam(value = "The username of the user to create or update.", required = true) @PathVariable("id") String username, @RequestBody User model) throws NotFoundException {
HttpStatus status = isPermitted(username);
if (status != null) {
@@ -162,8 +176,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns whether the user with the specified user ID is enabled.", notes = "Returns true or false based on whether the specified user is enabled or not.", response = Boolean.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User enabled status successfully retrieved."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to view this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/enabled"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
+ @ApiResponses({@ApiResponse(code = 200, message = "User enabled status successfully retrieved."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to view this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/enabled"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
public ResponseEntity<Boolean> usersIdEnabledGet(@ApiParam(value = "The ID of the user to retrieve the enabled status for.", required = true) @PathVariable("id") String id) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -184,8 +202,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the user's enabled state.", notes = "Sets the enabled state of the user with the specified user ID to the value of the flag parameter.", response = Boolean.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User enabled status successfully set."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/enabled/{flag}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
+ @ApiResponses({@ApiResponse(code = 200, message = "User enabled status successfully set."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/enabled/{flag}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
public ResponseEntity<Boolean> usersIdEnabledFlagPut(@ApiParam(value = "ID of the user to fetch", required = true) @PathVariable("id") String id, @ApiParam(value = "The value to set for the enabled status.", required = true) @PathVariable("flag") Boolean flag) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -213,8 +235,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns whether the user with the specified user ID is verified.", notes = "Returns true or false based on whether the specified user is verified or not.", response = Boolean.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User verified status successfully retrieved."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to view this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/verified"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
+ @ApiResponses({@ApiResponse(code = 200, message = "User verified status successfully retrieved."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to view this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/verified"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
public ResponseEntity<Boolean> usersIdVerifiedGet(@ApiParam(value = "The ID of the user to retrieve the verified status for.", required = true) @PathVariable("id") String id) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -235,8 +261,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the user's verified state.", notes = "Sets the verified state of the user with the specified user ID to the value of the flag parameter.", response = Boolean.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User verified status successfully set."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to verify or un-verify this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/verified/{flag}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
+ @ApiResponses({@ApiResponse(code = 200, message = "User verified status successfully set."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to verify or un-verify this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/verified/{flag}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
public ResponseEntity<Boolean> usersIdVerifiedFlagPut(@ApiParam(value = "ID of the user to fetch", required = true) @PathVariable("id") String id, @ApiParam(value = "The value to set for the verified status.", required = true) @PathVariable("flag") Boolean flag) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -264,8 +294,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns the roles for the user with the specified user ID.", notes = "Returns a collection of the user's roles.", response = Collection.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User roles successfully retrieved."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to view this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/roles"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
+ @ApiResponses({@ApiResponse(code = 200, message = "User roles successfully retrieved."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to view this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/roles"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
public ResponseEntity<Collection<String>> usersIdRolesGet(@ApiParam(value = "The ID of the user to retrieve the roles for.", required = true) @PathVariable("id") final String id) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -276,8 +310,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Adds a role to a user.", notes = "Assigns a new role to a user.", response = Boolean.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User role successfully added."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/roles/{role}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
+ @ApiResponses({@ApiResponse(code = 200, message = "User role successfully added."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/roles/{role}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
public ResponseEntity<Boolean> usersIdAddRole(@ApiParam(value = "ID of the user to add a role to", required = true) @PathVariable("id") String id, @ApiParam(value = "The user's new role.", required = true) @PathVariable("role") String role) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -304,8 +342,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Remove a user's role.", notes = "Removes a user's role.", response = Boolean.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User role successfully removed."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/roles/{role}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.DELETE})
+ @ApiResponses({@ApiResponse(code = 200, message = "User role successfully removed."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/roles/{role}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.DELETE})
public ResponseEntity<Boolean> usersIdRemoveRole(@ApiParam(value = "ID of the user to delete a role from", required = true) @PathVariable("id") String id, @ApiParam(value = "The user role to delete.", required = true) @PathVariable("role") String role) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -332,8 +374,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns the groups for the user with the specified user ID.", notes = "Returns a collection of the user's groups.", response = Set.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User groups successfully retrieved."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to view this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/groups"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
+ @ApiResponses({@ApiResponse(code = 200, message = "User groups successfully retrieved."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to view this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/groups"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
public ResponseEntity<Set<String>> usersIdGroupsGet(@ApiParam(value = "The ID of the user to retrieve the groups for.", required = true) @PathVariable("id") String id) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -355,8 +401,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Adds a user to a group.", notes = "Assigns user to a group.", response = Boolean.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User successfully added to group."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/groups/{group}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
+ @ApiResponses({@ApiResponse(code = 200, message = "User successfully added to group."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/groups/{group}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
public ResponseEntity<Boolean> usersIdAddGroup(@ApiParam(value = "ID of the user to add to a group", required = true) @PathVariable("id") String id, @ApiParam(value = "The user's new group.", required = true) @PathVariable("group") final String group) {
HttpStatus status = isPermitted(id);
if (status != null) {
@@ -383,8 +433,12 @@ public class UsersApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Removes a user from a group.", notes = "Removes a user from a group.", response = Boolean.class)
- @ApiResponses({@ApiResponse(code = 200, message = "User's group successfully removed."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."), @ApiResponse(code = 404, message = "User not found."), @ApiResponse(code = 500, message = "Unexpected error")})
- @RequestMapping(value = {"/profiles/{id}/groups/{group}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.DELETE})
+ @ApiResponses({@ApiResponse(code = 200, message = "User's group successfully removed."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to enable or disable this user."),
+ @ApiResponse(code = 404, message = "User not found."),
+ @ApiResponse(code = 500, message = "An unexpected error occurred.")})
+ @RequestMapping(value = {"{id}/groups/{group}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.DELETE})
public ResponseEntity<Boolean> usersIdRemoveGroup(@ApiParam(value = "ID of the user to remove from group", required = true) @PathVariable("id") final String id, @ApiParam(value = "The group to remove the user from.", required = true) @PathVariable("group") final String group) {
HttpStatus status = isPermitted(id);
if (status != null) {
diff --git a/src/main/java/org/nrg/xnat/configuration/AutomationConfig.java b/src/main/java/org/nrg/xnat/configuration/AutomationConfig.java
index 9920b3e9..a41ad015 100644
--- a/src/main/java/org/nrg/xnat/configuration/AutomationConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/AutomationConfig.java
@@ -2,6 +2,8 @@ package org.nrg.xnat.configuration;
import org.nrg.automation.runners.ScriptRunnerOutputAdapter;
import org.nrg.automation.services.ScriptRunnerService;
+import org.nrg.automation.services.ScriptService;
+import org.nrg.automation.services.ScriptTriggerService;
import org.nrg.automation.services.impl.DefaultScriptRunnerService;
import org.nrg.framework.exceptions.NrgServiceException;
import org.nrg.framework.orm.hibernate.HibernateEntityPackageList;
@@ -19,8 +21,8 @@ import java.util.Map;
public class AutomationConfig {
@Bean
- public ScriptRunnerService scriptRunnerService() {
- final DefaultScriptRunnerService service = new DefaultScriptRunnerService();
+ public ScriptRunnerService scriptRunnerService(final ScriptService scriptService, final ScriptTriggerService triggerService) {
+ final DefaultScriptRunnerService service = new DefaultScriptRunnerService(scriptService, triggerService);
service.setRunnerPackages(Collections.singletonList("org.nrg.automation.runners"));
return service;
}
diff --git a/src/main/java/org/nrg/xnat/configuration/OrmConfig.java b/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
index 519d9507..f91917d6 100644
--- a/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
@@ -7,7 +7,7 @@ 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.PrefixedTableNamingStrategy;
-import org.nrg.framework.utilities.Beans;
+import org.nrg.framework.beans.Beans;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.config.PropertiesFactoryBean;
diff --git a/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java b/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
index ecc8b48d..e461b620 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/PipelineEmailHandlerAbst.java
@@ -137,7 +137,7 @@ public abstract class PipelineEmailHandlerAbst extends WorkflowStatusEventHandle
if (StringUtils.isNotBlank(comments)) {
try {
- params.putAll(getSerializer().deserializeJson(comments, new TypeReference<HashMap<String, String>>(){}));
+ params.putAll(getSerializer().deserializeJson(comments, SerializerService.TYPE_REF_MAP_STRING_STRING));
} catch (Exception e1) {
// Do nothing. This isn't necessarily a problem.
params.put("comments",comments);
diff --git a/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java b/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
index 4b717f6b..b69d715b 100644
--- a/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/DatabaseConfig.java
@@ -4,7 +4,7 @@ import org.apache.commons.dbcp2.BasicDataSource;
import org.apache.commons.lang3.StringUtils;
import org.nrg.framework.exceptions.NrgServiceError;
import org.nrg.framework.exceptions.NrgServiceException;
-import org.nrg.framework.utilities.Beans;
+import org.nrg.framework.beans.Beans;
import org.postgresql.Driver;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
diff --git a/src/main/java/org/nrg/xnat/initialization/RootConfig.java b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
index 03dd06e6..f26e745a 100644
--- a/src/main/java/org/nrg/xnat/initialization/RootConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
@@ -8,11 +8,11 @@ import com.fasterxml.jackson.core.util.DefaultPrettyPrinter;
import com.fasterxml.jackson.databind.SerializationFeature;
import com.fasterxml.jackson.datatype.hibernate4.Hibernate4Module;
import org.apache.commons.beanutils.BeanUtils;
+import org.nrg.framework.beans.Beans;
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.prefs.beans.PreferenceBeanMixIn;
import org.nrg.xdat.preferences.SiteConfigPreferences;
import org.nrg.xnat.configuration.ApplicationConfig;
import org.nrg.xnat.helpers.prearchive.PrearcConfig;
@@ -40,7 +40,7 @@ import java.util.Map;
import java.util.Properties;
/**
- * Configuration for the XNAT root application context. This contains all of the basic infrastructure for initializing
+ * Configuration for the XNAT root application context. This contains all of the F infrastructure for initializing
* and bootstrapping the site, including data source configuration, transaction and session management, and site
* configuration preferences.
* <p>
@@ -102,7 +102,7 @@ public class RootConfig {
}
@Bean
- public Jackson2ObjectMapperBuilder objectMapperBuilder() {
+ public Jackson2ObjectMapperBuilder objectMapperBuilder() throws NrgServiceException {
return new Jackson2ObjectMapperBuilder()
.serializationInclusion(JsonInclude.Include.NON_NULL)
.failOnEmptyBeans(false)
@@ -113,10 +113,8 @@ public class RootConfig {
}
@Bean
- public Map<Class<?>, Class<?>> mixIns() {
- final Map<Class<?>, Class<?>> mixIns = new HashMap<>();
- mixIns.put(SiteConfigPreferences.class, PreferenceBeanMixIn.class);
- return mixIns;
+ public Map<Class<?>, Class<?>> mixIns() throws NrgServiceException {
+ return Beans.getMixIns();
}
@Bean
@@ -138,8 +136,8 @@ public class RootConfig {
}
@Bean
- public SerializerService serializerService() {
- return new SerializerService();
+ public SerializerService serializerService(final Jackson2ObjectMapperBuilder objectMapperBuilder) {
+ return new SerializerService(objectMapperBuilder);
}
@Bean
diff --git a/src/main/java/org/nrg/xnat/initialization/SecurityConfig.java b/src/main/java/org/nrg/xnat/initialization/SecurityConfig.java
index 6bd28e33..68b90f65 100644
--- a/src/main/java/org/nrg/xnat/initialization/SecurityConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/SecurityConfig.java
@@ -127,7 +127,7 @@ public class SecurityConfig {
public FilterSecurityInterceptorBeanPostProcessor filterSecurityInterceptorBeanPostProcessor(final SerializerService serializer, final SiteConfigPreferences preferences) throws IOException {
final Resource resource = RESOURCE_LOADER.getResource("classpath:META-INF/xnat/security/configured-urls.yaml");
try (final InputStream inputStream = resource.getInputStream()) {
- final HashMap<String, ArrayList<String>> urlMap = serializer.deserializeYaml(inputStream, TYPE_REFERENCE);
+ final HashMap<String, ArrayList<String>> urlMap = serializer.deserializeYaml(inputStream, SerializerService.TYPE_REF_MAP_STRING_LIST_STRING);
final FilterSecurityInterceptorBeanPostProcessor postProcessor = new FilterSecurityInterceptorBeanPostProcessor(preferences);
postProcessor.setOpenUrls(urlMap.get("openUrls"));
postProcessor.setAdminUrls(urlMap.get("adminUrls"));
@@ -236,7 +236,5 @@ public class SecurityConfig {
return list;
}
- private static final ResourceLoader RESOURCE_LOADER = new DefaultResourceLoader();
- private static final TypeReference<HashMap<String, ArrayList<String>>> TYPE_REFERENCE = new TypeReference<HashMap<String, ArrayList<String>>>() {
- };
-}
\ No newline at end of file
+ private static final ResourceLoader RESOURCE_LOADER = new DefaultResourceLoader();
+}
diff --git a/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java b/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
index a6ac8673..51b1ab3f 100644
--- a/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
+++ b/src/main/java/org/nrg/xnat/initialization/XnatWebAppInitializer.java
@@ -6,7 +6,7 @@ import org.apache.axis.transport.http.AxisServlet;
import org.apache.commons.lang3.StringUtils;
import org.apache.turbine.Turbine;
import org.nrg.framework.exceptions.NrgServiceRuntimeException;
-import org.nrg.framework.processors.XnatPluginBean;
+import org.nrg.framework.beans.XnatPluginBean;
import org.nrg.xdat.servlet.XDATAjaxServlet;
import org.nrg.xdat.servlet.XDATServlet;
import org.nrg.xnat.restlet.servlet.XNATRestletServlet;
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectUserListResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectUserListResource.java
index fd02b112..1ccc3039 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectUserListResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectUserListResource.java
@@ -13,6 +13,7 @@ package org.nrg.xnat.restlet.resources;
import org.apache.commons.lang3.StringUtils;
import org.nrg.config.services.ConfigService;
import org.nrg.framework.constants.Scope;
+import org.nrg.framework.services.SerializerService;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.security.helpers.Permissions;
@@ -101,7 +102,7 @@ public class ProjectUserListResource extends SecureResource {
final String config = configService.getConfigContents("user-resource-whitelist", "whitelist.json", Scope.Project, projectId);
if (!StringUtils.isBlank(config)) {
try {
- List<String> projectUserResourceWhitelist = getSerializer().deserializeJson(config, TYPE_REFERENCE_LIST_STRING);
+ List<String> projectUserResourceWhitelist = getSerializer().deserializeJson(config, SerializerService.TYPE_REF_LIST_STRING);
if (projectUserResourceWhitelist != null) {
return projectUserResourceWhitelist.contains(getUser().getUsername());
}
@@ -112,4 +113,4 @@ public class ProjectUserListResource extends SecureResource {
return false;
}
-}
\ No newline at end of file
+}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/RestMockCallMapRestlet.java b/src/main/java/org/nrg/xnat/restlet/resources/RestMockCallMapRestlet.java
index 86936594..7d509e39 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/RestMockCallMapRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/RestMockCallMapRestlet.java
@@ -10,10 +10,10 @@
*/
package org.nrg.xnat.restlet.resources;
-import com.fasterxml.jackson.core.type.TypeReference;
-import org.apache.commons.lang3.StringUtils;
import com.fasterxml.jackson.core.JsonFactory;
import com.fasterxml.jackson.databind.ObjectMapper;
+import org.apache.commons.lang3.StringUtils;
+import org.nrg.framework.services.SerializerService;
import org.nrg.xdat.XDAT;
import org.restlet.Context;
import org.restlet.data.MediaType;
@@ -33,7 +33,6 @@ import java.util.Map;
public class RestMockCallMapRestlet extends SecureResource {
- private final static TypeReference<HashMap<String, String>> TYPE_REFERENCE = new TypeReference<HashMap<String, String>>() {};
private final static ObjectMapper MAPPER = new ObjectMapper(new JsonFactory());
private final String _call;
@@ -47,7 +46,7 @@ public class RestMockCallMapRestlet extends SecureResource {
}
try {
- return MAPPER.readValue(configuration, TYPE_REFERENCE);
+ return MAPPER.readValue(configuration, SerializerService.TYPE_REF_MAP_STRING_STRING);
} catch (IOException ignored) {
return new HashMap<>();
}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
index 8d2adf27..eac158f4 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
@@ -1530,7 +1530,7 @@ public abstract class SecureResource extends Resource {
}
try {
- List<String> userResourceWhitelist = getSerializer().deserializeJson(config, TYPE_REFERENCE_LIST_STRING);
+ List<String> userResourceWhitelist = getSerializer().deserializeJson(config, SerializerService.TYPE_REF_LIST_STRING);
if (userResourceWhitelist != null) {
return userResourceWhitelist.contains(user.getUsername());
}
@@ -1542,8 +1542,6 @@ public abstract class SecureResource extends Resource {
return false;
}
- protected final static TypeReference<ArrayList<String>> TYPE_REFERENCE_LIST_STRING = new TypeReference<ArrayList<String>>() {};
-
private static final Map<String, List<FilteredResourceHandlerI>> handlers = Maps.newConcurrentMap();
/**
--
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