diff --git a/build.gradle b/build.gradle
index 59c17d7f913d915ee55ea9581866ed67a2052e60..9543b208da0846c055738baabc4beefc89371b18 100644
--- a/build.gradle
+++ b/build.gradle
@@ -465,7 +465,7 @@ dependencies {
runtime "org.codehaus.groovy.modules.http-builder:http-builder:0.7.2"
runtime "net.imagej:ij:1.50e"
runtime "net.bull.javamelody:javamelody-core:1.58.0"
- runtime "org.javassist:javassist:3.20.0-GA"
+ runtime "org.javassist:javassist:3.21.0-GA"
providedCompile "javax.servlet:javax.servlet-api:${vServletApi}"
diff --git a/src/main/java/org/nrg/dcm/id/ClassicDicomObjectIdentifier.java b/src/main/java/org/nrg/dcm/id/ClassicDicomObjectIdentifier.java
index 628f3aa02fe71beae3b53d9a95023d7977d87674..34b19420c88d3d664affb7fb24a7fade149288f9 100644
--- a/src/main/java/org/nrg/dcm/id/ClassicDicomObjectIdentifier.java
+++ b/src/main/java/org/nrg/dcm/id/ClassicDicomObjectIdentifier.java
@@ -19,31 +19,19 @@ import java.util.List;
import java.util.regex.Pattern;
public class ClassicDicomObjectIdentifier extends CompositeDicomObjectIdentifier {
- private static final ImmutableList<Extractor> aaExtractors, sessionExtractors, subjectExtractors;
- static {
- final ImmutableList.Builder<Extractor> aab = new ImmutableList.Builder<Extractor>();
- aab.add(new ContainedAssignmentExtractor(Tag.PatientComments, "AA", Pattern.CASE_INSENSITIVE),
- new ContainedAssignmentExtractor(Tag.StudyComments, "AA", Pattern.CASE_INSENSITIVE));
- aaExtractors = aab.build();
-
- final ImmutableList.Builder<Extractor> sessb = new ImmutableList.Builder<Extractor>();
- sessb.add(new ContainedAssignmentExtractor(Tag.PatientComments, "Session", Pattern.CASE_INSENSITIVE),
- new ContainedAssignmentExtractor(Tag.StudyComments, "Session", Pattern.CASE_INSENSITIVE),
- new TextExtractor(Tag.PatientID));
- sessionExtractors = sessb.build();
-
- final ImmutableList.Builder<Extractor> subjb = new ImmutableList.Builder<Extractor>();
- subjb.add(new ContainedAssignmentExtractor(Tag.PatientComments, "Subject", Pattern.CASE_INSENSITIVE),
- new ContainedAssignmentExtractor(Tag.StudyComments, "Subject", Pattern.CASE_INSENSITIVE),
- new TextExtractor(Tag.PatientName));
- subjectExtractors = subjb.build();
- }
-
- public static List<Extractor> getAAExtractors() { return aaExtractors; }
- public static List<Extractor> getSessionExtractors() { return sessionExtractors; }
- public static List<Extractor> getSubjectExtractors() { return subjectExtractors; }
+ private static final ImmutableList<Extractor> attributeExtractors = new ImmutableList.Builder<Extractor>().add(new ContainedAssignmentExtractor(Tag.PatientComments, "AA", Pattern.CASE_INSENSITIVE))
+ .add(new ContainedAssignmentExtractor(Tag.StudyComments, "AA", Pattern.CASE_INSENSITIVE))
+ .build();
+ private static final ImmutableList<Extractor> sessionExtractors = new ImmutableList.Builder<Extractor>().add(new ContainedAssignmentExtractor(Tag.PatientComments, "Session", Pattern.CASE_INSENSITIVE))
+ .add(new ContainedAssignmentExtractor(Tag.StudyComments, "Session", Pattern.CASE_INSENSITIVE))
+ .add(new TextExtractor(Tag.PatientID))
+ .build();
+ private static final ImmutableList<Extractor> subjectExtractors = new ImmutableList.Builder<Extractor>().add(new ContainedAssignmentExtractor(Tag.PatientComments, "Subject", Pattern.CASE_INSENSITIVE))
+ .add(new ContainedAssignmentExtractor(Tag.StudyComments, "Subject", Pattern.CASE_INSENSITIVE))
+ .add(new TextExtractor(Tag.PatientName))
+ .build();
public ClassicDicomObjectIdentifier() {
- super(new Xnat15DicomProjectIdentifier(), subjectExtractors, sessionExtractors, aaExtractors);
+ super(new Xnat15DicomProjectIdentifier(), subjectExtractors, sessionExtractors, attributeExtractors);
}
}
diff --git a/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java b/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
index 61e6b93553d00b12efb448fefa21429763f40c6b..cea37377703e06e0ce0081ee8a042cd69d5b7740 100644
--- a/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
+++ b/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
@@ -621,7 +621,7 @@ public class XnatPipelineLauncher {
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
xnatPipelineLauncher.setId(imageSession.getId());
@@ -651,24 +651,6 @@ public class XnatPipelineLauncher {
return xnatPipelineLauncher;
}
- public static XnatPipelineLauncher GetBareLauncherForExperiment(RunData data, Context context, XnatExperimentdata imageSession) throws Exception {
- XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data, context);
- xnatPipelineLauncher.setSupressNotification(true);
- UserI user = XDAT.getUserDetails();
- xnatPipelineLauncher.setParameter("useremail", user.getEmail());
- xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
- xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
-
- xnatPipelineLauncher.setId(imageSession.getId());
- xnatPipelineLauncher.setLabel(imageSession.getLabel());
- xnatPipelineLauncher.setDataType(imageSession.getXSIType());
- xnatPipelineLauncher.setExternalId(imageSession.getProject());
-
- return xnatPipelineLauncher;
- }
-
public static XnatPipelineLauncher GetLauncher(RunData data, Context context, XnatImagesessiondata imageSession) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = GetLauncherForExperiment(data, context, imageSession);
String path = imageSession.getArchivePath();
diff --git a/src/main/java/org/nrg/viewer/QCImageCreator.java b/src/main/java/org/nrg/viewer/QCImageCreator.java
index fc1fbec6d293c4a444ca399997a00ab4dc8931f0..5e252b89103ba269b7b3106692b394613804816b 100644
--- a/src/main/java/org/nrg/viewer/QCImageCreator.java
+++ b/src/main/java/org/nrg/viewer/QCImageCreator.java
@@ -49,7 +49,7 @@ public class QCImageCreator {
xnatPipelineLauncher.setParameter("session", mrSession.getId() );
xnatPipelineLauncher.setParameter("notify", "0" );
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
diff --git a/src/main/java/org/nrg/xapi/exceptions/InsufficientPrivilegesException.java b/src/main/java/org/nrg/xapi/exceptions/InsufficientPrivilegesException.java
new file mode 100644
index 0000000000000000000000000000000000000000..83f82face5dcf99744bbe8f4b376152b93df74cf
--- /dev/null
+++ b/src/main/java/org/nrg/xapi/exceptions/InsufficientPrivilegesException.java
@@ -0,0 +1,25 @@
+/*
+ * web: org.nrg.xapi.exceptions.DataFormatException
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2016, Washington University School of Medicine and Howard Hughes Medical Institute
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ */
+
+package org.nrg.xapi.exceptions;
+
+import org.springframework.http.HttpStatus;
+import org.springframework.web.bind.annotation.ResponseStatus;
+
+@ResponseStatus(HttpStatus.BAD_REQUEST)
+public class InsufficientPrivilegesException extends ApiException {
+ public InsufficientPrivilegesException(final String username) {
+ super(HttpStatus.BAD_REQUEST.value(), username);
+ }
+
+ @Override
+ public String getMessage() {
+ return String.format("The user %s has insufficient privileges for the requested operation.", super.getMessage());
+ }
+}
diff --git a/src/main/java/org/nrg/xapi/rest/XapiRestControllerAdvice.java b/src/main/java/org/nrg/xapi/rest/XapiRestControllerAdvice.java
index 9e59bd1b95e3904d91509eea244f2a5b150402ea..14a04d5ebe62e6f4e24fb4d5bd670c308bd1b1a6 100644
--- a/src/main/java/org/nrg/xapi/rest/XapiRestControllerAdvice.java
+++ b/src/main/java/org/nrg/xapi/rest/XapiRestControllerAdvice.java
@@ -17,6 +17,8 @@ import org.nrg.framework.exceptions.NrgServiceError;
import org.nrg.framework.exceptions.NrgServiceException;
import org.nrg.framework.exceptions.NrgServiceRuntimeException;
import org.nrg.xapi.exceptions.DataFormatException;
+import org.nrg.xapi.exceptions.InsufficientPrivilegesException;
+import org.nrg.xapi.exceptions.NotFoundException;
import org.nrg.xapi.exceptions.ResourceAlreadyExistsException;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -45,6 +47,11 @@ public class XapiRestControllerAdvice {
return handleException(request, exception.getMessage(), exception);
}
+ @ExceptionHandler(InsufficientPrivilegesException.class)
+ public ModelAndView handleInsufficientPrivilegesException(final HttpServletRequest request, final DataFormatException exception) {
+ return handleException(request, exception.getMessage(), exception);
+ }
+
@ExceptionHandler(ResourceAlreadyExistsException.class)
public ModelAndView handleDataFormatException(final HttpServletRequest request, final ResourceAlreadyExistsException exception) {
return handleException(request, exception.getMessage(), exception);
@@ -66,6 +73,11 @@ public class XapiRestControllerAdvice {
return handleException(HttpStatus.BAD_REQUEST, request, "Unable to find requested file or resource: " + exception.getMessage(), exception);
}
+ @ExceptionHandler(NotFoundException.class)
+ public ModelAndView handleNotFoundException(final HttpServletRequest request, final NotFoundException exception) {
+ return handleException(HttpStatus.BAD_REQUEST, request, exception.getMessage(), exception);
+ }
+
@ExceptionHandler(ConfigServiceException.class)
public ModelAndView handleConfigServiceException(final HttpServletRequest request, final ConfigServiceException exception) {
return handleException(HttpStatus.INTERNAL_SERVER_ERROR, request, "An error occurred when accessing the configuration service: " + exception.getMessage(), exception);
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 8e4577e3ef2bcaa59a63e3923eb5bdbbd6af344b..a748afe9bc02e272e0131a09729b9b54c05276be 100644
--- a/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java
+++ b/src/main/java/org/nrg/xapi/rest/notifications/NotificationsApi.java
@@ -12,12 +12,11 @@ package org.nrg.xapi.rest.notifications;
import io.swagger.annotations.*;
import org.apache.commons.lang3.StringUtils;
import org.nrg.framework.annotations.XapiRestController;
-import org.nrg.framework.exceptions.NrgServiceError;
-import org.nrg.framework.exceptions.NrgServiceRuntimeException;
import org.nrg.framework.services.SerializerService;
import org.nrg.prefs.exceptions.InvalidPreferenceName;
import org.nrg.xapi.exceptions.InitializationException;
import org.nrg.xdat.preferences.NotificationsPreferences;
+import org.nrg.xdat.preferences.SmtpServer;
import org.nrg.xdat.rest.AbstractXapiRestController;
import org.nrg.xdat.security.services.RoleHolder;
import org.nrg.xdat.security.services.UserManagementServiceI;
@@ -28,7 +27,6 @@ import org.slf4j.LoggerFactory;
import org.springframework.http.HttpStatus;
import org.springframework.http.MediaType;
import org.springframework.http.ResponseEntity;
-import org.springframework.mail.javamail.JavaMailSenderImpl;
import org.springframework.web.bind.annotation.*;
import javax.inject.Inject;
@@ -58,10 +56,9 @@ public class NotificationsApi extends AbstractXapiRestController {
+ "by calling the POST version of this method.";
@Inject
- public NotificationsApi(final UserManagementServiceI userManagementService, final RoleHolder roleHolder, final NotificationsPreferences notificationsPrefs, final JavaMailSenderImpl javaMailSender, final XnatAppInfo appInfo, final SerializerService serializer) {
+ public NotificationsApi(final UserManagementServiceI userManagementService, final RoleHolder roleHolder, final NotificationsPreferences notificationsPrefs, final XnatAppInfo appInfo, final SerializerService serializer) {
super(userManagementService, roleHolder);
_notificationsPrefs = notificationsPrefs;
- _javaMailSender = javaMailSender;
_appInfo = appInfo;
_serializer = serializer;
}
@@ -124,7 +121,7 @@ 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), SerializerService.TYPE_REF_MAP_STRING_STRING));
+ _notificationsPrefs.setSmtpServer(_serializer.deserializeJson(properties.getProperty(name), SmtpServer.class));
} else {
_notificationsPrefs.set(properties.getProperty(name), name);
}
@@ -137,32 +134,12 @@ public class NotificationsApi extends AbstractXapiRestController {
_log.error("An error occurred deserializing the preference: " + name + ", which is just lame.");
}
}
-
- // If any of the SMTP properties changed, then change the values for
- if (properties.containsKey("smtpServer") || properties.containsKey("host") || properties.containsKey("port") || properties.containsKey("protocol") || properties.containsKey("username") || properties.containsKey("password")) {
- final String host = _notificationsPrefs.getHostname();
- final int port = _notificationsPrefs.getPort();
- final String protocol = _notificationsPrefs.getProtocol();
- final String username = _notificationsPrefs.getUsername();
- final String password = _notificationsPrefs.getPassword();
-
- logConfigurationSubmit(host, port, protocol, username, password, properties);
-
- setHost(host, false);
- setPort(port);
- setProtocol(protocol);
- setUsername(username);
- setPassword(password);
-
- _javaMailSender.setJavaMailProperties(getSubmittedProperties(properties));
- }
-
return new ResponseEntity<>(HttpStatus.OK);
}
@ApiOperation(value = "Returns the full SMTP server configuration.",
- notes = "Returns the configuration as a map of the standard Java mail sender properties–host, port, protocol, username, and password–along with any extended properties required for the configuration, e.g. configuring SSL- or TLS-secured SMTP services.",
- response = Properties.class)
+ notes = "Returns the configuration as a map of the standard Java mail sender properties–host, port, protocol, username, and password–along with any extended properties required for the configuration, e.g. configuring SSL- or TLS-secured SMTP services.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "SMTP service configuration properties successfully retrieved."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set site configuration properties."),
@@ -176,39 +153,18 @@ public class NotificationsApi extends AbstractXapiRestController {
if (_log.isDebugEnabled()) {
_log.debug("User " + getSessionUser().getUsername() + " requested the site SMTP service configuration.");
}
- final Properties properties = new Properties();
- properties.setProperty("host", _javaMailSender.getHost());
- final int port = _javaMailSender.getPort();
- if (port > 0) {
- properties.setProperty("port", Integer.toString(port));
- }
- final String protocol = _javaMailSender.getProtocol();
- if (StringUtils.isNotBlank(protocol)) {
- properties.setProperty("protocol", protocol);
- }
- final String username = _javaMailSender.getUsername();
- if (StringUtils.isNotBlank(username)) {
- properties.setProperty("username", username);
- }
- final String password = _javaMailSender.getPassword();
- if (StringUtils.isNotBlank(password)) {
- properties.setProperty("password", password);
- }
- for (final String property : _javaMailSender.getJavaMailProperties().stringPropertyNames()) {
- properties.setProperty(property, _javaMailSender.getJavaMailProperties().getProperty(property));
- }
- return new ResponseEntity<>(properties, HttpStatus.OK);
+ return new ResponseEntity<>(_notificationsPrefs.getSmtpServer().asProperties(), HttpStatus.OK);
}
@ApiOperation(value = "Sets the mail service properties. This return the SMTP server configuration as it exists after being set.",
- notes = POST_PROPERTIES_NOTES,
- response = Properties.class)
+ notes = POST_PROPERTIES_NOTES,
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Mail service properties successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the mail service properties."),
@ApiResponse(code = 500, message = "Unexpected error")})
@RequestMapping(value = {"smtp"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.POST})
- public ResponseEntity<Properties> setAllMailProperties(@ApiParam("The value to set for the email host.") @RequestParam(value = "host", required = false, defaultValue = NOT_SET) final String host,
+ public ResponseEntity<Properties> setAllMailProperties(@ApiParam("The value to set for the email host.") @RequestParam(value = "hostname", required = false, defaultValue = NOT_SET) final String hostname,
@ApiParam("The value to set for the email port.") @RequestParam(value = "port", required = false, defaultValue = "-1") final int port,
@ApiParam("The value to set for the email username.") @RequestParam(value = "username", required = false, defaultValue = NOT_SET) final String username,
@ApiParam("The value to set for the email password.") @RequestParam(value = "password", required = false, defaultValue = NOT_SET) final String password,
@@ -220,28 +176,22 @@ public class NotificationsApi extends AbstractXapiRestController {
}
cleanProperties(properties);
- logConfigurationSubmit(host, port, username, password, protocol, properties);
+ logConfigurationSubmit(hostname, port, username, password, protocol, properties);
- setHost(host, true);
- setPort(port);
- setProtocol(protocol);
- setUsername(username);
- setPassword(password);
-
- _javaMailSender.setJavaMailProperties(getSubmittedProperties(properties));
+ _notificationsPrefs.setSmtpServer(new SmtpServer(hostname, port, protocol, username, password, properties));
return getSmtpServerProperties();
}
@ApiOperation(value = "Sets the submitted mail service properties. This returns the SMTP server configuration as it exists after being set.",
- notes = PUT_PROPERTIES_NOTES,
- response = Properties.class)
+ notes = PUT_PROPERTIES_NOTES,
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Mail service properties successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the mail service properties."),
@ApiResponse(code = 500, message = "Unexpected error")})
@RequestMapping(value = {"smtp"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
- public ResponseEntity<Properties> setSubmittedMailProperties(@ApiParam("The value to set for the email host.") @RequestParam(value = "host", required = false, defaultValue = NOT_SET) final String host,
+ public ResponseEntity<Properties> setSubmittedMailProperties(@ApiParam("The value to set for the email host.") @RequestParam(value = "hostname", required = false, defaultValue = NOT_SET) final String host,
@ApiParam("The value to set for the email port.") @RequestParam(value = "port", required = false, defaultValue = "-1") final int port,
@ApiParam("The value to set for the email username.") @RequestParam(value = "username", required = false, defaultValue = NOT_SET) final String username,
@ApiParam("The value to set for the email password.") @RequestParam(value = "password", required = false, defaultValue = NOT_SET) final String password,
@@ -254,23 +204,14 @@ public class NotificationsApi extends AbstractXapiRestController {
logConfigurationSubmit(host, port, username, password, protocol, properties);
- setHost(host, false);
- setPort(port);
- setProtocol(protocol);
- setUsername(username);
- setPassword(password);
- if (properties != null) {
- for (final String property : properties.stringPropertyNames()) {
- _javaMailSender.getJavaMailProperties().setProperty(property, properties.getProperty(property));
- }
- }
+ _notificationsPrefs.setSmtpServer(new SmtpServer(host, port, username, password, protocol, properties));
return getSmtpServerProperties();
}
@ApiOperation(value = "Sets the mail service host.",
- notes = "Sets the mail service host.",
- response = Properties.class)
+ notes = "Sets the mail service host.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Mail service host successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the mail service host."),
@@ -284,13 +225,13 @@ public class NotificationsApi extends AbstractXapiRestController {
if (_log.isInfoEnabled()) {
_log.info("User " + getSessionUser().getLogin() + " setting mail host to: " + host);
}
- setHost(host, true);
+ _notificationsPrefs.setSmtpHostname(host);
return getSmtpServerProperties();
}
@ApiOperation(value = "Sets the mail service port.",
- notes = "Sets the mail service port.",
- response = Properties.class)
+ notes = "Sets the mail service port.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Mail service port successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the mail service port."),
@@ -304,13 +245,13 @@ public class NotificationsApi extends AbstractXapiRestController {
if (_log.isInfoEnabled()) {
_log.info("User " + getSessionUser().getLogin() + " setting mail port to: " + port);
}
- setPort(port);
+ _notificationsPrefs.setSmtpPort(port);
return getSmtpServerProperties();
}
@ApiOperation(value = "Sets the mail service protocol.",
- notes = "Sets the mail service protocol.",
- response = Properties.class)
+ notes = "Sets the mail service protocol.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Mail service protocol successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the mail service protocol."),
@@ -324,13 +265,13 @@ public class NotificationsApi extends AbstractXapiRestController {
if (_log.isInfoEnabled()) {
_log.info("User " + getSessionUser().getLogin() + " setting mail protocol to: " + protocol);
}
- setProtocol(protocol);
+ _notificationsPrefs.setSmtpProtocol(protocol);
return getSmtpServerProperties();
}
@ApiOperation(value = "Sets the mail service username.",
- notes = "Sets the mail service username.",
- response = Properties.class)
+ notes = "Sets the mail service username.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Mail service username successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the mail service username."),
@@ -344,13 +285,13 @@ public class NotificationsApi extends AbstractXapiRestController {
if (_log.isInfoEnabled()) {
_log.info("User " + getSessionUser().getLogin() + " setting mail username to: " + username);
}
- setUsername(username);
+ _notificationsPrefs.setSmtpUsername(username);
return getSmtpServerProperties();
}
@ApiOperation(value = "Sets the mail service password.",
- notes = "Sets the mail service password.",
- response = Properties.class)
+ notes = "Sets the mail service password.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Mail service password successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the mail service password."),
@@ -364,20 +305,56 @@ public class NotificationsApi extends AbstractXapiRestController {
if (_log.isInfoEnabled()) {
_log.info("User " + getSessionUser().getLogin() + " setting mail password to: ********");
}
- setPassword(password);
+ _notificationsPrefs.setSmtpPassword(password);
return getSmtpServerProperties();
}
+ @ApiOperation(value = "Gets the value for a specified Java mail property.",
+ notes = "The value is always returned as a string.",
+ response = String.class)
+ @ApiResponses({@ApiResponse(code = 200, message = "Property found and returned."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to set the mail service properties."),
+ @ApiResponse(code = 404, message = "Specified key not found in the mail service properties."),
+ @ApiResponse(code = 500, message = "Unexpected error")})
+ @RequestMapping(value = {"smtp/property/{property}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
+ public ResponseEntity<String> getExtendedProperty(@ApiParam(value = "The mail property to be retrieved.", required = true) @PathVariable final String property) {
+ final HttpStatus status = isPermitted();
+ if (status != null) {
+ return new ResponseEntity<>(status);
+ }
+ if (!_notificationsPrefs.getSmtpServer().getMailProperties().containsKey(property)) {
+ return new ResponseEntity<>(HttpStatus.NOT_FOUND);
+ }
+ _log.info("User {} retrieving value for property {}", getSessionUser().getLogin(), property);
+ return new ResponseEntity<>(_notificationsPrefs.getSmtpMailProperty(property), HttpStatus.OK);
+ }
+
@ApiOperation(value = "Sets a Java mail property with the submitted name and value.",
- notes = "Setting a property to an empty value will remove the property.",
- response = Properties.class)
+ notes = "Setting a property to an existing value will overwrite the existing value. The value returned by this function contains the previous value (if any).",
+ response = String.class)
+ @ApiResponses({@ApiResponse(code = 200, message = "Property found and returned."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to set the mail service properties."),
+ @ApiResponse(code = 404, message = "Specified key not found in the mail service properties."),
+ @ApiResponse(code = 500, message = "Unexpected error")})
+ @RequestMapping(value = {"smtp/property/{property}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
+ public ResponseEntity<String> setExtendedProperty(@ApiParam(value = "The name of the extended mail property to set.", required = true) @PathVariable final String property,
+ @ApiParam(value = "The value to set for the extended mail property.", required = true) @RequestBody final String value) {
+ return setExtendedPropertyFromPath(property, value);
+ }
+
+ @ApiOperation(value = "Sets a Java mail property with the submitted name and value.",
+ notes = "Setting a property to an existing value will overwrite the existing value. The value returned by this function contains the previous value (if any).",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "Mail service password successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the mail service password."),
+ @ApiResponse(code = 404, message = "Specified key not found in the mail service properties."),
@ApiResponse(code = 500, message = "Unexpected error")})
@RequestMapping(value = {"smtp/property/{property}/{value}"}, produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.PUT})
- public ResponseEntity<Properties> setExtendedProperty(@ApiParam(value = "The value to set for the email password.", required = true) @PathVariable final String property,
- @ApiParam(value = "The value to set for the email password.", required = true) @PathVariable final String value) {
+ public ResponseEntity<String> setExtendedPropertyFromPath(@ApiParam(value = "The name of the extended mail property to set.", required = true) @PathVariable final String property,
+ @ApiParam(value = "The value to set for the extended mail property.", required = true) @PathVariable final String value) {
final HttpStatus status = isPermitted();
if (status != null) {
return new ResponseEntity<>(status);
@@ -385,13 +362,33 @@ public class NotificationsApi extends AbstractXapiRestController {
if (_log.isInfoEnabled()) {
_log.info("User " + getSessionUser().getLogin() + " setting mail password to: ********");
}
- setProperty(property, value);
- return getSmtpServerProperties();
+ return new ResponseEntity<>(_notificationsPrefs.setSmtpMailProperty(property, value), HttpStatus.OK);
+ }
+
+ @ApiOperation(value = "Removes the value for a specified Java mail property.",
+ notes = "This completely removes the specified mail property. The value returned by this function contains the previous value (if any).",
+ response = String.class)
+ @ApiResponses({@ApiResponse(code = 200, message = "Property found and returned."),
+ @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
+ @ApiResponse(code = 403, message = "Not authorized to set the mail service properties."),
+ @ApiResponse(code = 404, message = "Specified key not found in the mail service properties."),
+ @ApiResponse(code = 500, message = "Unexpected error")})
+ @RequestMapping(value = "smtp/property/{property}", produces = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.DELETE)
+ public ResponseEntity<String> removeExtendedProperty(@ApiParam(value = "The mail property to be removed.", required = true) @PathVariable final String property) {
+ final HttpStatus status = isPermitted();
+ if (status != null) {
+ return new ResponseEntity<>(status);
+ }
+ if (!_notificationsPrefs.getSmtpServer().getMailProperties().containsKey(property)) {
+ return new ResponseEntity<>(HttpStatus.NOT_FOUND);
+ }
+ _log.info("User {} removing value for property {}", getSessionUser().getLogin(), property);
+ return new ResponseEntity<>(_notificationsPrefs.removeSmtpMailProperty(property), HttpStatus.OK);
}
@ApiOperation(value = "Sets the email message for contacting help.",
- notes = "Sets the email message that people should receive when contacting help.",
- response = Void.class)
+ notes = "Sets the email message that people should receive when contacting help.",
+ response = Void.class)
@ApiResponses({@ApiResponse(code = 200, message = "Help email message successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the help email message."),
@@ -403,8 +400,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the email message for user registration.",
- notes = "Sets the email message that people should receive when they register. Link for email validation is auto-populated.",
- response = Properties.class)
+ notes = "Sets the email message that people should receive when they register. Link for email validation is auto-populated.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "User registration email message successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the user registration email message."),
@@ -416,8 +413,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the email message for forgot username.",
- notes = "Sets the email message that people should receive when they click that they forgot their username.",
- response = Properties.class)
+ notes = "Sets the email message that people should receive when they click that they forgot their username.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Forgot username email message successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the forgot username email message."),
@@ -429,8 +426,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the email message for password reset.",
- notes = "Sets the email message that people should receive when they click to reset their password. Link for password reset is auto-populated.",
- response = Properties.class)
+ notes = "Sets the email message that people should receive when they click to reset their password. Link for password reset is auto-populated.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Password reset message successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the password reset message."),
@@ -442,8 +439,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns the email message for contacting help.",
- notes = "This returns the email message that people should receive when contacting help.",
- response = String.class)
+ notes = "This returns the email message that people should receive when contacting help.",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "Email message for contacting help successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get email message for contacting help."),
@@ -454,8 +451,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns the email message for user registration.",
- notes = "This returns the email message that people should receive when they register. Link for email validation is auto-populated.",
- response = String.class)
+ notes = "This returns the email message that people should receive when they register. Link for email validation is auto-populated.",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "Email message for user registration successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get email message for user registration."),
@@ -466,8 +463,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns the email message for forgot username.",
- notes = "This returns the email message that people should receive when they click that they forgot their username.",
- response = String.class)
+ notes = "This returns the email message that people should receive when they click that they forgot their username.",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "Email message for forgot username successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get email message for forgot username."),
@@ -478,8 +475,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns the email message for password reset.",
- notes = "This returns the email message that people should receive when they click to reset their password. Link for password reset is auto-populated.",
- response = String.class)
+ notes = "This returns the email message that people should receive when they click to reset their password. Link for password reset is auto-populated.",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "Email message for password reset successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get email message for password reset."),
@@ -490,8 +487,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets whether admins should be notified of user registration.",
- notes = "Sets whether admins should be notified of user registration.",
- response = Void.class)
+ notes = "Sets whether admins should be notified of user registration.",
+ response = Void.class)
@ApiResponses({@ApiResponse(code = 200, message = "Whether admins should be notified of user registration successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set whether admins should be notified of user registration."),
@@ -503,8 +500,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets whether admins should be notified of pipeline processing submit.",
- notes = "Sets whether admins should be notified of pipeline processing submit.",
- response = Properties.class)
+ notes = "Sets whether admins should be notified of pipeline processing submit.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Whether admins should be notified of pipeline processing submit successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set whether admins should be notified of pipeline processing submit."),
@@ -516,8 +513,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets whether admins should be notified of project access requests.",
- notes = "Sets whether admins should be notified of project access requests.",
- response = Properties.class)
+ notes = "Sets whether admins should be notified of project access requests.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Whether admins should be notified of project access requests successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set whether admins should be notified of project access requests."),
@@ -529,8 +526,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets whether admins should be notified of session transfer.",
- notes = "Sets whether admins should be notified of session transfer by user.",
- response = Properties.class)
+ notes = "Sets whether admins should be notified of session transfer by user.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Whether admins should be notified of session transfer successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set whether admins should be notified of session transfer."),
@@ -542,8 +539,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns whether admins should be notified of user registration.",
- notes = "This returns whether admins should be notified of user registration.",
- response = Boolean.class)
+ notes = "This returns whether admins should be notified of user registration.",
+ response = Boolean.class)
@ApiResponses({@ApiResponse(code = 200, message = "Email message for contacting help successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get email message for contacting help."),
@@ -554,8 +551,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns whether admins should be notified of pipeline processing submit.",
- notes = "This returns whether admins should be notified of pipeline processing submit.",
- response = Boolean.class)
+ notes = "This returns whether admins should be notified of pipeline processing submit.",
+ response = Boolean.class)
@ApiResponses({@ApiResponse(code = 200, message = "Email message for user registration successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get email message for user registration."),
@@ -566,8 +563,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns whether admins should be notified of project access requests.",
- notes = "This returns whether admins should be notified of project access requests.",
- response = Boolean.class)
+ notes = "This returns whether admins should be notified of project access requests.",
+ response = Boolean.class)
@ApiResponses({@ApiResponse(code = 200, message = "Email message for forgot username successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get email message for forgot username."),
@@ -578,8 +575,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns whether admins should be notified of session transfer.",
- notes = "This returns whether admins should be notified of session transfer.",
- response = Boolean.class)
+ notes = "This returns whether admins should be notified of session transfer.",
+ response = Boolean.class)
@ApiResponses({@ApiResponse(code = 200, message = "Email message for password reset successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get email message for password reset."),
@@ -590,8 +587,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets whether non-users should be able to subscribe to notifications.",
- notes = "Sets whether non-users should be able to subscribe to notifications.",
- response = Properties.class)
+ notes = "Sets whether non-users should be able to subscribe to notifications.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Whether non-users should be able to subscribe to notifications."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set whether non-users should be able to subscribe to notifications."),
@@ -603,8 +600,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns whether non-users should be able to subscribe to notifications.",
- notes = "This returns whether non-users should be able to subscribe to notifications.",
- response = Boolean.class)
+ notes = "This returns whether non-users should be able to subscribe to notifications.",
+ response = Boolean.class)
@ApiResponses({@ApiResponse(code = 200, message = "Whether non-users should be able to subscribe to notifications successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get whether non-users should be able to subscribe to notifications."),
@@ -615,8 +612,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the email addresses for error notifications.",
- notes = "Sets the email addresses that should be subscribed to error notifications.",
- response = Void.class)
+ notes = "Sets the email addresses that should be subscribed to error notifications.",
+ response = Void.class)
@ApiResponses({@ApiResponse(code = 200, message = "Error subscribers successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the error subscribers."),
@@ -628,8 +625,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the email addresses for issue notifications.",
- notes = "Sets the email addresses that should be subscribed to issue notifications.",
- response = Properties.class)
+ notes = "Sets the email addresses that should be subscribed to issue notifications.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Issue subscribers successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the issue subscribers."),
@@ -641,8 +638,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the email addresses for new user notifications.",
- notes = "Sets the email addresses that should be subscribed to new user notifications.",
- response = Properties.class)
+ notes = "Sets the email addresses that should be subscribed to new user notifications.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "New user subscribers successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the new user subscribers."),
@@ -654,8 +651,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Sets the email addresses for update notifications.",
- notes = "Sets the email addresses that should be subscribed to update notifications.",
- response = Properties.class)
+ notes = "Sets the email addresses that should be subscribed to update notifications.",
+ response = Properties.class)
@ApiResponses({@ApiResponse(code = 200, message = "Update subscribers successfully set."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to set the update subscribers."),
@@ -667,8 +664,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns list of email addresses subscribed to error notifications.",
- notes = "This returns a list of all the email addresses that are subscribed to receive error notifications.",
- response = String.class)
+ notes = "This returns a list of all the email addresses that are subscribed to receive error notifications.",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "Error notification subscribers successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get subscribers for email notifications."),
@@ -679,8 +676,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns list of email addresses subscribed to issue notifications.",
- notes = "This returns a list of all the email addresses that are subscribed to receive issue notifications.",
- response = String.class)
+ notes = "This returns a list of all the email addresses that are subscribed to receive issue notifications.",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "Issue notification subscribers successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get subscribers for email notifications."),
@@ -691,8 +688,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns list of email addresses subscribed to new user notifications.",
- notes = "This returns a list of all the email addresses that are subscribed to receive new user notifications.",
- response = String.class)
+ notes = "This returns a list of all the email addresses that are subscribed to receive new user notifications.",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "New user notification subscribers successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get subscribers for email notifications."),
@@ -703,8 +700,8 @@ public class NotificationsApi extends AbstractXapiRestController {
}
@ApiOperation(value = "Returns list of email addresses subscribed to update notifications.",
- notes = "This returns a list of all the email addresses that are subscribed to receive update notifications.",
- response = String.class)
+ notes = "This returns a list of all the email addresses that are subscribed to receive update notifications.",
+ response = String.class)
@ApiResponses({@ApiResponse(code = 200, message = "Update notification subscribers successfully returned."),
@ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."),
@ApiResponse(code = 403, message = "Not authorized to get subscribers for email notifications."),
@@ -714,51 +711,27 @@ public class NotificationsApi extends AbstractXapiRestController {
return new ResponseEntity<>(_notificationsPrefs.getEmailRecipientUpdate(), HttpStatus.OK);
}
- protected Properties getSubmittedProperties(final Properties properties) {
- // Set all of the submitted properties.
- final Properties javaMailProperties = new Properties();
- if (properties != null) {
- for (final String property : properties.stringPropertyNames()) {
- final String value = properties.getProperty(property);
- if (StringUtils.isNotBlank(value)) {
- javaMailProperties.setProperty(property, value);
- }
- }
- }
-
- // Find any existing properties that weren't submitted...
- final Properties existing = _javaMailSender.getJavaMailProperties();
- for (final String property : existing.stringPropertyNames()) {
- if (!javaMailProperties.containsKey(property)) {
- // Set the value to "", this will remove the property.
- javaMailProperties.setProperty(property, "");
- }
- }
- return javaMailProperties;
- }
-
private Properties convertToProperties(final Map<String, Object> preferenceMap) throws IOException {
final Properties properties = new Properties();
for (final String key : preferenceMap.keySet()) {
- final Object object = preferenceMap.get(key);
- String tempVal = "";
- if(object!=null){
- if(String.class.isAssignableFrom(object.getClass())){
- tempVal = (String)object;
- }
- else{
+ final Object object = preferenceMap.get(key);
+ String tempVal = "";
+ if (object != null) {
+ if (String.class.isAssignableFrom(object.getClass())) {
+ tempVal = (String) object;
+ } else {
tempVal = _serializer.toJson(object);
}
}
- final String value = tempVal;
+ final String value = tempVal;
properties.setProperty(key, value);
}
return properties;
}
private void cleanProperties(final Properties properties) {
- if (properties.containsKey("host")) {
- properties.remove("host");
+ if (properties.containsKey("hostname")) {
+ properties.remove("hostname");
}
if (properties.containsKey("port")) {
properties.remove("port");
@@ -772,47 +745,20 @@ public class NotificationsApi extends AbstractXapiRestController {
if (properties.containsKey("password")) {
properties.remove("password");
}
- }
-
- private void setHost(final String host, final boolean freakOutIfBlank) {
- if (freakOutIfBlank && StringUtils.isBlank(host)) {
- throw new NrgServiceRuntimeException(NrgServiceError.ConfigurationError, "You can not set the SMTP server address to an empty value!");
- }
- if (StringUtils.isNotBlank(host)) {
- _javaMailSender.setHost(host);
- }
- }
-
- private void setPort(final int port) {
- if (port != -1) {
- _javaMailSender.setPort(port);
+ if (properties.containsKey("smtpHostname")) {
+ properties.remove("smtpHostname");
}
- }
-
- private void setProtocol(final String protocol) {
- if (!StringUtils.equals(NOT_SET, protocol)) {
- _javaMailSender.setProtocol(protocol);
+ if (properties.containsKey("smtpPort")) {
+ properties.remove("smtpPort");
}
- }
-
- private void setUsername(final String username) {
- if (!StringUtils.equals(NOT_SET, username)) {
- _javaMailSender.setUsername(username);
+ if (properties.containsKey("smtpProtocol")) {
+ properties.remove("smtpProtocol");
}
- }
-
- private void setPassword(final String password) {
- if (!StringUtils.equals(NOT_SET, password)) {
- _javaMailSender.setPassword(password);
+ if (properties.containsKey("smtpUsername")) {
+ properties.remove("smtpUsername");
}
- }
-
- private void setProperty(final String property, final String value) {
- final Properties properties = _javaMailSender.getJavaMailProperties();
- if (properties.containsKey(property) && StringUtils.isBlank(value)) {
- properties.remove(property);
- } else {
- properties.setProperty(property, value);
+ if (properties.containsKey("smtpPassword")) {
+ properties.remove("smtpPassword");
}
}
@@ -834,11 +780,10 @@ public class NotificationsApi extends AbstractXapiRestController {
}
}
- private static final Logger _log = LoggerFactory.getLogger(NotificationsApi.class);
- private static final String NOT_SET = "NotSet";
+ private static final Logger _log = LoggerFactory.getLogger(NotificationsApi.class);
+ private static final String NOT_SET = "NotSet";
private final NotificationsPreferences _notificationsPrefs;
- private final JavaMailSenderImpl _javaMailSender;
private final XnatAppInfo _appInfo;
private final SerializerService _serializer;
}
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 b45ddd15faa5362e3fe0405ee3e4182bdf363db2..708cc46249d6eb43cc3409d2eb321ab1d2ff73b2 100644
--- a/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
+++ b/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
@@ -13,14 +13,17 @@ import com.google.common.base.Joiner;
import io.swagger.annotations.*;
import org.apache.commons.lang3.StringUtils;
import org.nrg.framework.annotations.XapiRestController;
+import org.nrg.framework.exceptions.NrgServiceRuntimeException;
import org.nrg.prefs.exceptions.InvalidPreferenceName;
+import org.nrg.xapi.exceptions.ApiException;
import org.nrg.xapi.exceptions.InitializationException;
+import org.nrg.xapi.exceptions.InsufficientPrivilegesException;
+import org.nrg.xapi.exceptions.NotFoundException;
import org.nrg.xdat.preferences.SiteConfigPreferences;
import org.nrg.xdat.rest.AbstractXapiRestController;
import org.nrg.xdat.security.services.RoleHolder;
import org.nrg.xdat.security.services.UserManagementServiceI;
import org.nrg.xnat.services.XnatAppInfo;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
import org.nrg.xnat.utils.XnatHttpUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
@@ -102,7 +105,7 @@ public class SiteConfigApi extends AbstractXapiRestController {
@ApiResponse(code = 403, message = "Not authorized to set site configuration properties."),
@ApiResponse(code = 500, message = "Unexpected error")})
@RequestMapping(consumes = {MediaType.APPLICATION_FORM_URLENCODED_VALUE, MediaType.APPLICATION_JSON_VALUE}, method = RequestMethod.POST)
- public ResponseEntity<Void> setSiteConfigProperties(@ApiParam(value = "The map of site configuration properties to be set.", required = true) @RequestBody final Map<String, String> properties) throws InitializationException {
+ public ResponseEntity<Void> setSiteConfigProperties(@ApiParam(value = "The map of site configuration properties to be set.", required = true) @RequestBody final Map<String, String> properties) throws ApiException, InitializationException {
final HttpStatus status = isPermitted();
if (status != null) {
return new ResponseEntity<>(status);
@@ -116,6 +119,12 @@ public class SiteConfigApi extends AbstractXapiRestController {
if (isInitializing && name.equals("initialized")) {
continue;
}
+ if (name.equals("receivedFileUser")) {
+ final HttpStatus setStatus = setReceivedFileUser(properties.get(name));
+ if (setStatus != null) {
+ return new ResponseEntity<>(setStatus);
+ }
+ }
_preferences.set(properties.get(name), name);
if (_log.isInfoEnabled()) {
_log.info("Set property {} to value: {}", name, properties.get(name));
@@ -127,10 +136,7 @@ public class SiteConfigApi extends AbstractXapiRestController {
// If we're initializing...
if (isInitializing) {
- // Make the final initialization call.
- initialize();
-
- // Now make the initialized setting true.
+ // Now make the initialized setting true. This will kick off the initialized event handler.
_preferences.setInitialized(true);
}
@@ -191,7 +197,8 @@ public class SiteConfigApi extends AbstractXapiRestController {
@ApiResponse(code = 403, message = "Not authorized to set site configuration properties."),
@ApiResponse(code = 500, message = "Unexpected error")})
@RequestMapping(value = "{property}", consumes = {MediaType.TEXT_PLAIN_VALUE, MediaType.APPLICATION_JSON_VALUE}, produces = MediaType.APPLICATION_JSON_VALUE, method = RequestMethod.POST)
- public ResponseEntity<Void> setSiteConfigProperty(@ApiParam(value = "The property to be set.", required = true) @PathVariable("property") final String property, @ApiParam("The value to be set for the property.") @RequestBody final String value) throws InitializationException {
+ public ResponseEntity<Void> setSiteConfigProperty(@ApiParam(value = "The property to be set.", required = true) @PathVariable("property") final String property,
+ @ApiParam("The value to be set for the property.") @RequestBody final String value) throws InitializationException, ApiException {
final HttpStatus status = isPermitted();
if (status != null) {
return new ResponseEntity<>(status);
@@ -202,8 +209,12 @@ public class SiteConfigApi extends AbstractXapiRestController {
}
if (StringUtils.equals("initialized", property) && StringUtils.equals("true", value)) {
- initialize();
_preferences.setInitialized(true);
+ } else if (StringUtils.equals("receivedFileUser", property)) {
+ final HttpStatus setStatus = setReceivedFileUser(value);
+ if (setStatus != null) {
+ return new ResponseEntity<>(setStatus);
+ }
} else {
try {
_preferences.set(value, property);
@@ -268,6 +279,24 @@ public class SiteConfigApi extends AbstractXapiRestController {
return new ResponseEntity<>(_appInfo.getFormattedUptime(), HttpStatus.OK);
}
+ private HttpStatus setReceivedFileUser(final String value) throws InsufficientPrivilegesException, NotFoundException {
+ try {
+ _preferences.setReceivedFileUser(value);
+ } catch (NrgServiceRuntimeException e) {
+ switch (e.getServiceError()) {
+ case PermissionsViolation:
+ throw new InsufficientPrivilegesException(e.getMessage());
+ case UserNotFoundError:
+ throw new NotFoundException("No user with the name " + e.getMessage() + " was found.");
+ case Unknown:
+ default:
+ _log.error("An unknown error occurred trying to set the received file user to value " + value, e);
+ return HttpStatus.INTERNAL_SERVER_ERROR;
+ }
+ }
+ return null;
+ }
+
private Map<String, Object> getPreferences() {
if (!_hasFoundPreferences) {
return _preferences.getPreferenceMap();
@@ -277,17 +306,6 @@ public class SiteConfigApi extends AbstractXapiRestController {
return preferences;
}
- private void initialize() throws InitializationException {
- // In the case where the application hasn't yet been initialized, this operation should mean that the system is
- // being initialized from the set-up page. In that case, we need to propagate a few properties to the arc-spec
- // persistence to support
- try {
- ArcSpecManager.initialize(getSessionUser());
- } catch (Exception e) {
- throw new InitializationException(e);
- }
- }
-
private static final Logger _log = LoggerFactory.getLogger(SiteConfigApi.class);
private final SiteConfigPreferences _preferences;
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 248ccc1c70af79ff7f5d411e0cc6548acc29d68f..0f3412df29486d33ea110440649b4630339e21f3 100644
--- a/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
+++ b/src/main/java/org/nrg/xapi/rest/users/UsersApi.java
@@ -134,20 +134,30 @@ public class UsersApi extends AbstractXapiRestController {
} else {
username = principal.toString();
}
- final Map<String, Object> sessionData = new HashMap<>();
final List<SessionInformation> sessions = _sessionRegistry.getAllSessions(principal, false);
+
+ // Sometimes there are no sessions, which is weird but OK, we don't want to see those entries.
+ final int count = sessions.size();
+ if (count == 0) {
+ continue;
+ }
+
+ // Now add user with a session or more to the list of active users.
final ArrayList<String> sessionIds = new ArrayList<>();
for (final SessionInformation session : sessions) {
sessionIds.add(session.getSessionId());
}
+
+ final Map<String, Object> sessionData = new HashMap<>();
sessionData.put("sessions", sessionIds);
- sessionData.put("count", sessions.size());
+ sessionData.put("count", count);
+
activeUsers.put(username, sessionData);
}
return new ResponseEntity<>(activeUsers, HttpStatus.OK);
}
- @ApiOperation(value = "Get information about active sessions for the indicated user.", notes = "Returns a map containing a list of session IDs usernames for users that have at least one currently active session, i.e. logged in or associated with a valid application session. This also includes the number of active sessions for each user.", response = String.class, responseContainer = "List")
+ @ApiOperation(value = "Get information about active sessions for the indicated user.", notes = "Returns a map containing a list of session IDs and usernames for users that have at least one currently active session, i.e. logged in or associated with a valid application session. This also includes the number of active sessions for each user.", response = String.class, responseContainer = "List")
@ApiResponses({@ApiResponse(code = 200, message = "A list of active users."),
@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."),
diff --git a/src/main/java/org/nrg/xnat/archive/Transfer.java b/src/main/java/org/nrg/xnat/archive/Transfer.java
index 367114e0ff833282c7d38412d25fd9cdfbaf1e1b..a8f6c11cebbf3bf790d00460145f6de65151a514 100644
--- a/src/main/java/org/nrg/xnat/archive/Transfer.java
+++ b/src/main/java/org/nrg/xnat/archive/Transfer.java
@@ -130,7 +130,7 @@ public class Transfer {
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
xnatPipelineLauncher.setParameter("adminemail", admin_email);
xnatPipelineLauncher.setParameter("xnatserver", system);
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
xnatPipelineLauncher.setParameter("sessionType", mr.getXSIType());
xnatPipelineLauncher.setParameter("xnat_project", mr.getProject());
xnatPipelineLauncher.setParameter("logDir", XDAT.getSiteConfigPreferences().getCachePath() + "logs" + "/" + "transfer");
diff --git a/src/main/java/org/nrg/xnat/configuration/NotificationsConfig.java b/src/main/java/org/nrg/xnat/configuration/NotificationsConfig.java
index 188e2c9878f997848ee33dd8ccc26b44b316e9f5..9b98c513ad4482a0408200c11fdf07920f387bda 100644
--- a/src/main/java/org/nrg/xnat/configuration/NotificationsConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/NotificationsConfig.java
@@ -18,6 +18,7 @@ import org.nrg.notify.renderers.ChannelRenderer;
import org.nrg.notify.renderers.NrgMailChannelRenderer;
import org.nrg.xdat.preferences.NotificationsPreferences;
import org.nrg.xdat.preferences.SiteConfigPreferences;
+import org.nrg.xdat.preferences.SmtpServer;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
@@ -27,7 +28,6 @@ import java.io.IOException;
import java.util.Collections;
import java.util.HashMap;
import java.util.Map;
-import java.util.Properties;
@Configuration
@ComponentScan({"org.nrg.mail.services", "org.nrg.notify.services.impl", "org.nrg.notify.daos"})
@@ -35,20 +35,16 @@ public class NotificationsConfig {
@Bean
public JavaMailSenderImpl mailSender(final NotificationsPreferences preferences) throws IOException, SiteConfigurationException {
- final Map<String, String> smtp = preferences.getSmtpServer();
+ final SmtpServer smtp = preferences.getSmtpServer();
final JavaMailSenderImpl sender = new JavaMailSenderImpl();
if(smtp!=null) {
- sender.setHost(StringUtils.defaultIfBlank(smtp.remove("host"), "localhost"));
- sender.setPort(Integer.parseInt(StringUtils.defaultIfBlank(smtp.remove("port"), "25")));
- sender.setUsername(StringUtils.defaultIfBlank(smtp.remove("username"), ""));
- sender.setPassword(StringUtils.defaultIfBlank(smtp.remove("password"), ""));
- sender.setProtocol(StringUtils.defaultIfBlank(smtp.remove("protocol"), "smtp"));
- if (smtp.size() > 0) {
- final Properties properties = new Properties();
- for (final String property : smtp.keySet()) {
- properties.setProperty(property, smtp.get(property));
- }
- sender.setJavaMailProperties(properties);
+ sender.setHost(StringUtils.defaultIfBlank(smtp.getHostname(), "localhost"));
+ sender.setPort(smtp.getPort());
+ sender.setUsername(StringUtils.defaultIfBlank(smtp.getUsername(), ""));
+ sender.setPassword(StringUtils.defaultIfBlank(smtp.getPassword(), ""));
+ sender.setProtocol(StringUtils.defaultIfBlank(smtp.getProtocol(), "smtp"));
+ if (smtp.getMailProperties().size() > 0) {
+ sender.setJavaMailProperties(smtp.getMailProperties());
}
}
return sender;
diff --git a/src/main/java/org/nrg/xnat/configuration/PreferencesConfig.java b/src/main/java/org/nrg/xnat/configuration/PreferencesConfig.java
index 2c6e157899bcbd7fbd049cfec81eaaf20b45836a..8262729f829ec5f21d5dd7083e311c5bdf0b2235 100644
--- a/src/main/java/org/nrg/xnat/configuration/PreferencesConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/PreferencesConfig.java
@@ -9,26 +9,19 @@
package org.nrg.xnat.configuration;
-import org.nrg.config.exceptions.SiteConfigurationException;
import org.nrg.config.services.ConfigService;
-import org.nrg.config.services.SiteConfigurationService;
import org.nrg.config.services.UserConfigurationService;
import org.nrg.config.services.impl.DefaultConfigService;
import org.nrg.config.services.impl.DefaultUserConfigurationService;
import org.nrg.prefs.configuration.NrgPrefsConfiguration;
-import org.nrg.prefs.services.NrgPreferenceService;
import org.nrg.prefs.services.PreferenceService;
-import org.nrg.xdat.preferences.SiteConfigPreferences;
import org.nrg.xnat.resolvers.XnatPreferenceEntityResolver;
import org.springframework.context.annotation.Bean;
import org.springframework.context.annotation.ComponentScan;
import org.springframework.context.annotation.Configuration;
import org.springframework.context.annotation.Import;
-import org.springframework.core.env.Environment;
import java.io.IOException;
-import java.lang.reflect.Constructor;
-import java.lang.reflect.InvocationTargetException;
@Configuration
@ComponentScan("org.nrg.config.daos")
@@ -45,26 +38,6 @@ public class PreferencesConfig {
return new DefaultUserConfigurationService(configService());
}
- @Bean
- public SiteConfigurationService siteConfigurationService(final SiteConfigPreferences preferences, final NrgPreferenceService nrgPreferenceService, final ConfigService configService, final Environment environment) throws ClassNotFoundException, IllegalAccessException, InstantiationException, SiteConfigurationException {
- final Class<? extends SiteConfigurationService> clazz = Class.forName(preferences.getSiteConfigurationService()).asSubclass(SiteConfigurationService.class);
- try {
- @SuppressWarnings("unchecked")
- final Constructor<? extends SiteConfigurationService> constructor = clazz.getConstructor(NrgPreferenceService.class, Environment.class);
- return constructor.newInstance(nrgPreferenceService, environment);
- } catch (NoSuchMethodException | InvocationTargetException ignored) {
- // No worries, it just doesn't have that constructor.
- }
- try {
- @SuppressWarnings("unchecked")
- final Constructor<? extends SiteConfigurationService> constructor = clazz.getConstructor(ConfigService.class, Environment.class);
- return constructor.newInstance(configService, environment);
- } catch (NoSuchMethodException | InvocationTargetException ignored) {
- // No worries, it just doesn't have that constructor.
- }
- return clazz.newInstance();
- }
-
@Bean
public XnatPreferenceEntityResolver defaultResolver(final PreferenceService preferenceService) throws IOException {
return new XnatPreferenceEntityResolver(preferenceService);
diff --git a/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java b/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
index d867e03f2066aa53eaf10b398a51cb16d319aa06..21a34ed92c9ad77fd5728451369faaa406af0fe4 100644
--- a/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/SchedulerConfig.java
@@ -71,12 +71,12 @@ public class SchedulerConfig implements SchedulingConfigurer {
_service.triggerEvent(new PreferenceEvent("inactivityBeforeLockout", String.valueOf(_siteConfigPreferences.getInactivityBeforeLockout())));
_service.triggerEvent(new PreferenceEvent("maxFailedLoginsLockoutDuration", String.valueOf(_siteConfigPreferences.getMaxFailedLoginsLockoutDuration())));
_service.triggerEvent(new PreferenceEvent("emailPrefix", String.valueOf(_notificationsPreferences.getEmailPrefix())));
- _service.triggerEvent(new PreferenceEvent("host", String.valueOf(_notificationsPreferences.getHostname())));
+ _service.triggerEvent(new PreferenceEvent("smtpHostname", String.valueOf(_notificationsPreferences.getSmtpHostname())));
_service.triggerEvent(new PreferenceEvent("requireLogin", String.valueOf(_siteConfigPreferences.getRequireLogin())));
- _service.triggerEvent(new PreferenceEvent("security.channel", String.valueOf(_siteConfigPreferences.getSecurityChannel())));
+ _service.triggerEvent(new PreferenceEvent("securityChannel", String.valueOf(_siteConfigPreferences.getSecurityChannel())));
_service.triggerEvent(new PreferenceEvent("passwordExpirationType", String.valueOf(_siteConfigPreferences.getPasswordExpirationType())));
_service.triggerEvent(new PreferenceEvent("archivePath", String.valueOf(_siteConfigPreferences.getArchivePath())));
- _service.triggerEvent(new PreferenceEvent("security.services.role.default", String.valueOf(_siteConfigPreferences.getRoleService())));
+ _service.triggerEvent(new PreferenceEvent("roleService", String.valueOf(_siteConfigPreferences.getRoleService())));
_service.triggerEvent(new PreferenceEvent("checksums", String.valueOf(_siteConfigPreferences.getChecksums())));
_service.triggerEvent(new PreferenceEvent("sitewidePetTracers", String.valueOf(_siteConfigPreferences.getSitewidePetTracers())));
diff --git a/src/main/java/org/nrg/xnat/event/listeners/SiteConfigPreferenceHandler.java b/src/main/java/org/nrg/xnat/event/listeners/SiteConfigPreferenceHandler.java
index 6e29b30a2ce6807a764f9b02b7b54b7a75c3a4fc..3af8c555615ffb14eb4170a414ac32cd31a76c1f 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/SiteConfigPreferenceHandler.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/SiteConfigPreferenceHandler.java
@@ -9,8 +9,6 @@
package org.nrg.xnat.event.listeners;
-import org.apache.commons.logging.Log;
-import org.apache.commons.logging.LogFactory;
import org.nrg.prefs.events.AbstractPreferenceHandler;
import org.nrg.prefs.events.PreferenceHandlerMethod;
import org.nrg.xdat.preferences.PreferenceEvent;
@@ -24,35 +22,31 @@ import java.util.List;
@Service
public class SiteConfigPreferenceHandler extends AbstractPreferenceHandler<PreferenceEvent> {
- private String _toolId=SiteConfigPreferences.SITE_CONFIG_TOOL_ID;
- private final List<PreferenceHandlerMethod> _methods = new ArrayList<>();
-
- @Inject
- public SiteConfigPreferenceHandler(final EventBus eventBus){
- super(eventBus);
- }
-
- @Override
- public String getToolId() {
- return _toolId;
- }
-
- @Override
- public void setToolId(String toolId) {
- _toolId=toolId;
- }
-
- @Override
- public List<PreferenceHandlerMethod> getMethods(){
- return _methods;
- }
-
- @Override
- public void addMethod(PreferenceHandlerMethod method){
- _methods.add(method);
- }
-
- private static final Log _log = LogFactory.getLog(SiteConfigPreferenceHandler.class);
-
-
+ private String _toolId = SiteConfigPreferences.SITE_CONFIG_TOOL_ID;
+ private final List<PreferenceHandlerMethod> _methods = new ArrayList<>();
+
+ @Inject
+ public SiteConfigPreferenceHandler(final EventBus eventBus) {
+ super(eventBus);
+ }
+
+ @Override
+ public String getToolId() {
+ return _toolId;
+ }
+
+ @Override
+ public void setToolId(String toolId) {
+ _toolId = toolId;
+ }
+
+ @Override
+ public List<PreferenceHandlerMethod> getMethods() {
+ return _methods;
+ }
+
+ @Override
+ public void addMethod(PreferenceHandlerMethod method) {
+ _methods.add(method);
+ }
}
diff --git a/src/main/java/org/nrg/xnat/event/listeners/methods/FeatureServicesHandlerMethod.java b/src/main/java/org/nrg/xnat/event/listeners/methods/FeatureServicesHandlerMethod.java
index a3f8a0913902a48180013ebbfcb5ce66578c48ae..4e682c4820850895521381ae0443d3d17b45b6c0 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/methods/FeatureServicesHandlerMethod.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/methods/FeatureServicesHandlerMethod.java
@@ -11,8 +11,6 @@ package org.nrg.xnat.event.listeners.methods;
import com.google.common.collect.ImmutableList;
import org.nrg.xdat.security.helpers.Features;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
import org.springframework.stereotype.Component;
import java.util.Arrays;
@@ -46,7 +44,6 @@ public class FeatureServicesHandlerMethod extends AbstractSiteConfigPreferenceHa
Features.setFeatureRepositoryServiceToSiteConfigPreference();
}
- private static final Logger _log = LoggerFactory.getLogger(FeatureServicesHandlerMethod.class);
- private static final List<String> PREFERENCES = ImmutableList.copyOf(Arrays.asList("security.services.feature.default", "security.services.featureRepository.default"));
+ private static final List<String> PREFERENCES = ImmutableList.copyOf(Arrays.asList("featureService", "featureRepositoryService"));
}
diff --git a/src/main/java/org/nrg/xnat/event/listeners/methods/InitializedHandlerMethod.java b/src/main/java/org/nrg/xnat/event/listeners/methods/InitializedHandlerMethod.java
new file mode 100644
index 0000000000000000000000000000000000000000..ea96b98c6e4d6c8c0ba66599f5e04e164c89d4ee
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/event/listeners/methods/InitializedHandlerMethod.java
@@ -0,0 +1,106 @@
+/*
+ * web: org.nrg.xnat.event.listeners.methods.RequiredChannelHandlerMethod
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2016, Washington University School of Medicine and Howard Hughes Medical Institute
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ */
+
+package org.nrg.xnat.event.listeners.methods;
+
+import com.google.common.collect.ImmutableList;
+import org.nrg.framework.exceptions.NrgServiceError;
+import org.nrg.framework.exceptions.NrgServiceRuntimeException;
+import org.nrg.xapi.exceptions.InitializationException;
+import org.nrg.xdat.preferences.SiteConfigPreferences;
+import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import org.nrg.xnat.utils.XnatUserProvider;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.util.Collections;
+import java.util.List;
+import java.util.Map;
+
+@Component
+public class InitializedHandlerMethod extends AbstractSiteConfigPreferenceHandlerMethod {
+ @Autowired
+ public InitializedHandlerMethod(final SiteConfigPreferences preferences, final XnatUserProvider primaryAdminUserProvider) {
+ super(primaryAdminUserProvider);
+ _preferences = preferences;
+ }
+
+ @Override
+ public List<String> getHandledPreferences() {
+ return PREFERENCES;
+ }
+
+ @Override
+ public void handlePreferences(final Map<String, String> values) {
+ if (values.containsKey(INITIALIZED)) {
+ handlePreference(INITIALIZED, values.get(INITIALIZED));
+ }
+ }
+
+ @Override
+ public void handlePreference(final String preference, final String value) {
+ if (PREFERENCES.contains(preference)) {
+ try {
+ initialize();
+ } catch (InitializationException e) {
+ throw new NrgServiceRuntimeException(NrgServiceError.Unknown, "An error occurred attempting to complete system initialization", e);
+ }
+ }
+ }
+
+ private void initialize() throws InitializationException {
+ final String adminEmail = _preferences.getAdminEmail();
+ final String archivePath = _preferences.getArchivePath();
+ final String buildPath = _preferences.getBuildPath();
+ final String cachePath = _preferences.getCachePath();
+ final boolean enableCsrfToken = _preferences.getEnableCsrfToken();
+ final String ftpPath = _preferences.getFtpPath();
+ final String pipelinePath = _preferences.getPipelinePath();
+ final String prearchivePath = _preferences.getPrearchivePath();
+ final boolean requireLogin = _preferences.getRequireLogin();
+ final String siteId = _preferences.getSiteId();
+ final String siteUrl = _preferences.getSiteUrl();
+ final boolean userRegistration = _preferences.getUserRegistration();
+
+ // TODO: We may actually need to put a null check in here and make this a Future that circles back once everything is properly initialized.
+ final StringBuilder buffer = new StringBuilder("Preparing to complete system initialization with the final property settings of:").append(System.lineSeparator());
+ buffer.append(" * adminEmail: ").append(adminEmail).append(System.lineSeparator());
+ buffer.append(" * archivePath: ").append(archivePath).append(System.lineSeparator());
+ buffer.append(" * buildPath: ").append(buildPath).append(System.lineSeparator());
+ buffer.append(" * cachePath: ").append(cachePath).append(System.lineSeparator());
+ buffer.append(" * enableCsrfToken: ").append(enableCsrfToken).append(System.lineSeparator());
+ buffer.append(" * ftpPath: ").append(ftpPath).append(System.lineSeparator());
+ buffer.append(" * pipelinePath: ").append(pipelinePath).append(System.lineSeparator());
+ buffer.append(" * prearchivePath: ").append(prearchivePath).append(System.lineSeparator());
+ buffer.append(" * requireLogin: ").append(requireLogin).append(System.lineSeparator());
+ buffer.append(" * siteId: ").append(siteId).append(System.lineSeparator());
+ buffer.append(" * siteUrl: ").append(siteUrl).append(System.lineSeparator());
+ buffer.append(" * userRegistration: ").append(userRegistration).append(System.lineSeparator());
+
+ _log.info(buffer.toString());
+
+ // In the case where the application hasn't yet been initialized, this operation should mean that the system is
+ // being initialized from the set-up page. In that case, we need to propagate a few properties to the arc-spec
+ // persistence to support
+ try {
+ ArcSpecManager.initialize(getAdminUser());
+ } catch (Exception e) {
+ throw new InitializationException(e);
+ }
+ }
+
+ private static final Logger _log = LoggerFactory.getLogger(InitializedHandlerMethod.class);
+
+ private static final String INITIALIZED = "initialized";
+ private static final List<String> PREFERENCES = ImmutableList.copyOf(Collections.singletonList(INITIALIZED));
+
+ private final SiteConfigPreferences _preferences;
+}
diff --git a/src/main/java/org/nrg/xnat/event/listeners/methods/RequiredChannelHandlerMethod.java b/src/main/java/org/nrg/xnat/event/listeners/methods/RequiredChannelHandlerMethod.java
index 87950b798488e691267e0f97acdebc9b58b4ad98..287d41d7f2e46d7c1d7d2e0d35e1ef103c5501fc 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/methods/RequiredChannelHandlerMethod.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/methods/RequiredChannelHandlerMethod.java
@@ -50,7 +50,7 @@ public class RequiredChannelHandlerMethod extends AbstractSiteConfigPreferenceHa
_filter.setRequiredChannel(_preferences.getSecurityChannel());
}
- private static final List<String> PREFERENCES = ImmutableList.copyOf(Collections.singletonList("security.channel"));
+ private static final List<String> PREFERENCES = ImmutableList.copyOf(Collections.singletonList("securityChannel"));
private final SiteConfigPreferences _preferences;
private final TranslatingChannelProcessingFilter _filter;
diff --git a/src/main/java/org/nrg/xnat/event/listeners/methods/RoleServicesHandlerMethod.java b/src/main/java/org/nrg/xnat/event/listeners/methods/RoleServicesHandlerMethod.java
index 2299b72fd24f19647dcc6dd2e7dff6852a432894..0c503241ca87e1c0be17ba11f45f5b80db6bfa99 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/methods/RoleServicesHandlerMethod.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/methods/RoleServicesHandlerMethod.java
@@ -77,7 +77,7 @@ public class RoleServicesHandlerMethod extends AbstractSiteConfigPreferenceHandl
}
private static final Logger _log = LoggerFactory.getLogger(RoleServicesHandlerMethod.class);
- private static final List<String> PREFERENCES = ImmutableList.copyOf(Arrays.asList("security.services.role.default", "security.services.roleRepository.default"));
+ private static final List<String> PREFERENCES = ImmutableList.copyOf(Arrays.asList("roleService", "roleRepositoryService"));
private final SiteConfigPreferences _preferences;
private final RoleHolder _roleHolder;
diff --git a/src/main/java/org/nrg/xnat/event/listeners/methods/SmtpHandlerMethod.java b/src/main/java/org/nrg/xnat/event/listeners/methods/SmtpHandlerMethod.java
index 296967f00b7f30eba2d6b18ccc69596b8c78e9c9..e21fd61e7362fed74797ec46aa52a9a050950175 100644
--- a/src/main/java/org/nrg/xnat/event/listeners/methods/SmtpHandlerMethod.java
+++ b/src/main/java/org/nrg/xnat/event/listeners/methods/SmtpHandlerMethod.java
@@ -10,8 +10,9 @@
package org.nrg.xnat.event.listeners.methods;
import com.google.common.collect.ImmutableList;
-import org.nrg.mail.services.MailService;
+import org.apache.commons.lang.StringUtils;
import org.nrg.xdat.preferences.NotificationsPreferences;
+import org.nrg.xdat.preferences.SmtpServer;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.mail.javamail.JavaMailSenderImpl;
import org.springframework.stereotype.Component;
@@ -21,10 +22,9 @@ import java.util.*;
@Component
public class SmtpHandlerMethod extends AbstractNotificationsPreferenceHandlerMethod {
@Autowired
- public SmtpHandlerMethod(final NotificationsPreferences preferences, final JavaMailSenderImpl mailSender, final MailService mailService) {
+ public SmtpHandlerMethod(final NotificationsPreferences preferences, final JavaMailSenderImpl mailSender) {
_preferences = preferences;
- this._mailSender = mailSender;
- _mailService = mailService;
+ _mailSender = mailSender;
}
@Override
@@ -34,48 +34,44 @@ public class SmtpHandlerMethod extends AbstractNotificationsPreferenceHandlerMet
@Override
public void handlePreferences(final Map<String, String> values) {
- if (!Collections.disjoint(PREFERENCES, values.keySet())) {
- updateSmtp();
- }
+ updateSmtp();
}
@Override
public void handlePreference(final String preference, final String value) {
- if (PREFERENCES.contains(preference)) {
- updateSmtp();
- }
+ updateSmtp();
}
private void updateSmtp() {
- final Properties oldMailProperties = _mailSender.getJavaMailProperties();
-
- final boolean smtpEnabled = _preferences.getSmtpEnabled();
- final boolean smtpAuth = _preferences.getSmtpAuth();
- final boolean startTls = _preferences.getSmtpStartTls();
- final String sslTrust = _preferences.getSmtpSSLTrust();
-
- _mailSender.setHost(_preferences.getHostname());
- _mailSender.setPort(_preferences.getPort());
- _mailSender.setUsername(_preferences.getUsername());
- _mailSender.setPassword(_preferences.getPassword());
- _mailSender.setProtocol(_preferences.getProtocol());
- _mailService.setSmtpEnabled(smtpEnabled);
-
- oldMailProperties.setProperty("smtp.enabled", String.valueOf(smtpEnabled));
- oldMailProperties.setProperty("mail.smtp.auth", String.valueOf(smtpAuth));
- oldMailProperties.setProperty("mail.smtp.starttls.enable", String.valueOf(startTls));
-
- if (sslTrust != null) {
- oldMailProperties.setProperty("mail.smtp.ssl.trust", sslTrust);
+ final SmtpServer smtpServer = _preferences.getSmtpServer();
+
+ _mailSender.setHost(smtpServer.getHostname());
+ _mailSender.setPort(smtpServer.getPort());
+ _mailSender.setUsername(smtpServer.getUsername());
+ _mailSender.setPassword(smtpServer.getPassword());
+ _mailSender.setProtocol(smtpServer.getProtocol());
+
+ if (!smtpServer.getSmtpAuth()) {
+ _mailSender.setJavaMailProperties(SMTP_AUTH_DISABLED);
+ } else {
+ final Properties properties = new Properties();
+ properties.setProperty(SmtpServer.SMTP_KEY_AUTH, "true");
+ if (smtpServer.getSmtpStartTls()) {
+ properties.setProperty(SmtpServer.SMTP_KEY_STARTTLS_ENABLE, "true");
+ }
+ if (StringUtils.isNotBlank(smtpServer.getSmtpSslTrust())) {
+ properties.setProperty(SmtpServer.SMTP_KEY_SSL_TRUST, smtpServer.getSmtpSslTrust());
+ }
+ properties.putAll(smtpServer.getMailProperties());
+ _mailSender.setJavaMailProperties(properties);
}
-
- _mailSender.setJavaMailProperties(oldMailProperties);
}
- private static final List<String> PREFERENCES = ImmutableList.copyOf(Arrays.asList("smtp.enabled", "host", "port", "username", "password", "protocol", "smtp.enabled", "mail.smtp.auth", "mail.smtp.starttls.enable", "mail.smtp.ssl.trust"));
+ private static final List<String> PREFERENCES = ImmutableList.copyOf(Arrays.asList("smtpEnabled", "smtpHostname", "smtpPort", "smtpUsername", "smtpPassword", "smtpProtocol", "smtpAuth", "smtpStartTls", "smtpSslTrust"));
+ private static final Properties SMTP_AUTH_DISABLED = new Properties() {{
+ setProperty(SmtpServer.SMTP_KEY_AUTH, "false");
+ }};
private final NotificationsPreferences _preferences;
private final JavaMailSenderImpl _mailSender;
- private final MailService _mailService;
-
}
diff --git a/src/main/java/org/nrg/xnat/event/listeners/methods/XnatUserProviderPreferenceHandlerMethod.java b/src/main/java/org/nrg/xnat/event/listeners/methods/XnatUserProviderPreferenceHandlerMethod.java
new file mode 100644
index 0000000000000000000000000000000000000000..91807ce7f3755651dbcb3083eb7c4d30ee4eb360
--- /dev/null
+++ b/src/main/java/org/nrg/xnat/event/listeners/methods/XnatUserProviderPreferenceHandlerMethod.java
@@ -0,0 +1,52 @@
+/*
+ * web: org.nrg.xnat.event.listeners.methods.ReceivedFileUserPreferenceHandlerMethod
+ * XNAT http://www.xnat.org
+ * Copyright (c) 2016, Washington University School of Medicine
+ * All Rights Reserved
+ *
+ * Released under the Simplified BSD.
+ */
+
+package org.nrg.xnat.event.listeners.methods;
+
+import com.google.common.collect.Maps;
+import org.apache.commons.lang3.StringUtils;
+import org.nrg.xnat.utils.XnatUserProvider;
+import org.springframework.beans.factory.annotation.Autowired;
+import org.springframework.stereotype.Component;
+
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Map;
+
+@Component
+public class XnatUserProviderPreferenceHandlerMethod extends AbstractSiteConfigPreferenceHandlerMethod {
+ @Autowired
+ public XnatUserProviderPreferenceHandlerMethod(final Map<String, XnatUserProvider> providers) {
+ _providers = Maps.newHashMap(providers);
+ }
+
+ @Override
+ public List<String> getHandledPreferences() {
+ return new ArrayList<>(_providers.keySet());
+ }
+
+ @Override
+ public void handlePreferences(final Map<String, String> values) {
+ for (final String key : values.keySet()) {
+ handlePreference(key, values.get(key));
+ }
+ }
+
+ @Override
+ public void handlePreference(final String preference, final String value) {
+ if (_providers.containsKey(preference)) {
+ final XnatUserProvider provider = _providers.get(preference);
+ if (!StringUtils.equals(value, provider.getLogin())) {
+ provider.setLogin(value);
+ }
+ }
+ }
+
+ private final Map<String, XnatUserProvider> _providers;
+}
diff --git a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcUtils.java b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcUtils.java
index dd82e99f24ebf2428c5ac12c894475166e752c73..2850af58f7279873a5dbe325ca857ca125c28088 100644
--- a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcUtils.java
+++ b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcUtils.java
@@ -15,6 +15,7 @@ import org.apache.commons.io.filefilter.DirectoryFileFilter;
import org.apache.commons.lang3.StringUtils;
import org.nrg.config.entities.Configuration;
import org.nrg.framework.constants.Scope;
+import org.nrg.xapi.exceptions.InsufficientPrivilegesException;
import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.ArcProjectI;
import org.nrg.xdat.om.ArcProject;
@@ -223,12 +224,11 @@ public class PrearcUtils {
public static File getPrearcDir(final UserI user, final String project, final boolean allowUnassigned) throws Exception {
String prearcPath;
String prearchRootPref = XDAT.getSiteConfigPreferences().getPrearchivePath();
- String prearchRootArcSpec = ArcSpecManager.GetInstance().getGlobalPrearchivePath();
if (project == null || project.equals(COMMON)) {
if (allowUnassigned || user == null || Roles.isSiteAdmin(user)) {
prearcPath = prearchRootPref;
} else {
- throw new InvalidPermissionException("user " + user.getUsername() + " does not have permission to access the Unassigned directory ");
+ throw new InsufficientPrivilegesException(user.getUsername());
}
} else {
//Refactored to remove unnecessary database hits. It only needs to hit the xnat_projectdata table if the query is using a project alias rather than a project id. TO
@@ -306,8 +306,8 @@ public class PrearcUtils {
* @param project If the project is null, it is the unassigned project
* project abbreviation or alias
* @return true if the user has permissions to access the project, false otherwise
- * @throws Exception
- * @throws IOException
+ * @throws Exception When something goes wrong.
+ * @throws IOException When an error occurs reading or writing data.
*/
@SuppressWarnings("unused")
public static boolean validUser(final UserI user, final String project, final boolean allowUnassigned) throws Exception {
@@ -525,7 +525,7 @@ public class PrearcUtils {
}
public static String makeUri(final String urlBase, final String timestamp, final String folderName) {
- return StringUtils.join(new String[]{urlBase, "/", timestamp, "/", folderName});
+ return StringUtils.join(urlBase, "/", timestamp, "/", folderName);
}
public static Map<String, Object> parseURI(final String uri) throws MalformedURLException {
@@ -533,7 +533,7 @@ public class PrearcUtils {
}
public static String buildURI(final String project, final String timestamp, final String folderName) {
- return StringUtils.join(new String[]{"/prearchive/projects/", (project == null) ? PrearcUtils.COMMON : project, "/", timestamp, "/", folderName});
+ return StringUtils.join("/prearchive/projects/", (project == null) ? PrearcUtils.COMMON : project, "/", timestamp, "/", folderName);
}
public static XFTTable convertArrayLtoTable(ArrayList<ArrayList<Object>> rows) {
@@ -809,8 +809,8 @@ public class PrearcUtils {
* @param session The session to be locked.
* @param filename The filename to be locked.
* @return PrearcFileLock
- * @throws SessionFileLockException
- * @throws IOException
+ * @throws SessionFileLockException When an attempt is made to access a locked file.
+ * @throws IOException When an error occurs reading or writing data.
*/
public static PrearcFileLock lockFile(final SessionDataTriple session, final String filename) throws SessionFileLockException, IOException {
//putting these in a subdirectory of the cache space
@@ -858,19 +858,26 @@ public class PrearcUtils {
synchronized (syncLock) {
//synchronized to prevent overlap with .lockFile()
- if (name.exists() && (name.list() == null || name.list().length == 0)) {
- try {
- FileUtils.deleteDirectory(name);
-
- if (timestamp.exists() && (timestamp.list() == null || timestamp.list().length == 0)) {
- FileUtils.deleteDirectory(timestamp);
-
- if (project.exists() && (project.list() == null || project.list().length == 0)) {
- FileUtils.deleteDirectory(project);
+ if (name.exists()) {
+ final String[] names = name.list();
+ if (names == null || names.length == 0) {
+ try {
+ FileUtils.deleteDirectory(name);
+ if (timestamp.exists()) {
+ final String[] timestamps = timestamp.list();
+ if (timestamps == null || timestamps.length == 0) {
+ FileUtils.deleteDirectory(timestamp);
+ if (project.exists()) {
+ final String[] projects = project.list();
+ if (projects == null || projects.length == 0) {
+ FileUtils.deleteDirectory(project);
+ }
+ }
+ }
}
+ } catch (IOException e) {
+ logger.error("Couldn't clean temporary lock directories in the cache folder.", e);
}
- } catch (IOException e) {
- logger.error("Couldn't clean temporary lock directories in the cache folder.", e);
}
}
}
diff --git a/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java b/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java
index e3570b3b257bf5b6352e0c0dd4977f489ce8f32b..a30abd942b135c57b84b489e62b32d6c93c3ad98 100644
--- a/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java
+++ b/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java
@@ -64,7 +64,7 @@ public class TriggerPipelines implements Callable<Boolean> {
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
xnatPipelineLauncher.setParameter("sessionType", expt.getXSIType());
xnatPipelineLauncher.setParameter("xnat_project", expt.getProject());
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java
index a3cf5b56aa5aead85dff37aa8ff7c64a49b77d0d..d2d064b1c34d6b249192abca06343874556ad332 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java
@@ -279,7 +279,7 @@ public class ProjtExptPipelineResource extends SecureResource {
hasParams.add("userfullname");
xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
hasParams.add("adminemail");
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
hasParams.add("mailhost");
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
hasParams.add("xnatserver");
@@ -394,7 +394,7 @@ public class ProjtExptPipelineResource extends SecureResource {
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ManagePipeline.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ManagePipeline.java
index 74253496a9cf28f35b9cc89f25f4f73951c5f962..7dd6b042a21da18da5a7ad35f97d3f6abab99a6f 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ManagePipeline.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ManagePipeline.java
@@ -379,7 +379,7 @@ public class ManagePipeline extends SecureAction {
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
xnatPipelineLauncher.setPipelineName(pipeline_path);
String exptLabel = item.getStringProperty("label");
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/PipelineActions.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/PipelineActions.java
index 46433009b3c0685fe250c89638a6859b256eb12c..208a02ea5629e32b62554af8f8ea9f024834bee9 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/PipelineActions.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/PipelineActions.java
@@ -204,7 +204,7 @@ public class PipelineActions extends SecureAction{
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
String emailsStr = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("emailField",data));
if (emailsStr != null) {
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/QDECAction.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/QDECAction.java
index d753fc8fb8f5ca0b7826a156d97a64a41ce51947..0888c646368e5ba06abb7266e32bfe79caa8081c 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/QDECAction.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/QDECAction.java
@@ -208,7 +208,7 @@ public class QDECAction extends ListingAction{
param = parameters.addNewParameter();
param.setName("mailhost");
- param.addNewValues().setUnique( XDAT.getNotificationsPreferences().getSmtpServer().get("host"));
+ param.addNewValues().setUnique( XDAT.getNotificationsPreferences().getSmtpServer().getHostname());
return parameters;
diff --git a/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java b/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java
index a5a704ab0be9698755353015ef4927b9774cbd85..2f9bdc180ebb630cdf00b5d06f188cbf66e543fb 100644
--- a/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java
+++ b/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java
@@ -15,6 +15,7 @@ import org.nrg.xdat.model.ArcProjectI;
import org.nrg.xdat.om.ArcArchivespecification;
import org.nrg.xdat.preferences.NotificationsPreferences;
import org.nrg.xdat.preferences.SiteConfigPreferences;
+import org.nrg.xdat.preferences.SmtpServer;
import org.nrg.xft.event.EventDetails;
import org.nrg.xft.event.EventUtils;
import org.nrg.xft.security.UserI;
@@ -31,7 +32,6 @@ import java.io.IOException;
import java.nio.file.Paths;
import java.util.ArrayList;
import java.util.List;
-import java.util.Map;
/**
* @author timo
@@ -65,7 +65,9 @@ public class ArcSpecManager {
String cachePath = arcSpec.getGlobalCachePath();
if (cachePath!=null){
File f = new File(cachePath,"archive_specification.xml");
- f.getParentFile().mkdirs();
+ if (!f.getParentFile().mkdirs()) {
+ throw new RuntimeException("Failed to create working file " + f.getAbsolutePath() + ", please check permissions and file system.");
+ }
FileWriter fw = new FileWriter(f);
arcSpec.toXML(fw, true);
@@ -120,12 +122,11 @@ public class ArcSpecManager {
arcSpec.setSiteUrl(siteConfigPreferences.getSiteUrl());
}
- final Map<String, String> smtpServer = notificationsPreferences.getSmtpServer();
- if (smtpServer != null && smtpServer.containsKey("host")) {
- if (logger.isInfoEnabled()) {
- logger.info("Setting SMTP host to: {}", smtpServer.get("host"));
- }
- arcSpec.setSmtpHost(smtpServer.get("host"));
+ final SmtpServer smtpServer = notificationsPreferences.getSmtpServer();
+ if (smtpServer != null) {
+ final String hostname = smtpServer.getHostname();
+ logger.info("Setting SMTP host to: {}", hostname);
+ arcSpec.setSmtpHost(hostname);
}
if (logger.isInfoEnabled()) {
diff --git a/src/main/java/org/nrg/xnat/utils/XnatUserProvider.java b/src/main/java/org/nrg/xnat/utils/XnatUserProvider.java
index 0314d6fa3d8ffe6aeddb894c61561e9bbbe8b93d..ad38c9aba15da102ed4062868cfcab9c551c980e 100644
--- a/src/main/java/org/nrg/xnat/utils/XnatUserProvider.java
+++ b/src/main/java/org/nrg/xnat/utils/XnatUserProvider.java
@@ -9,6 +9,7 @@
package org.nrg.xnat.utils;
+import org.apache.commons.lang3.StringUtils;
import org.nrg.framework.exceptions.NrgServiceError;
import org.nrg.framework.exceptions.NrgServiceRuntimeException;
import org.nrg.xdat.security.helpers.Users;
@@ -27,7 +28,8 @@ import javax.inject.Provider;
@Component
public class XnatUserProvider implements Provider<UserI> {
public XnatUserProvider(final String login) {
- _login = login;
+ _logger.debug("Initializing user provider with login {}", login);
+ setLogin(login);
}
/**
@@ -35,16 +37,17 @@ public class XnatUserProvider implements Provider<UserI> {
*/
@Override
public UserI get() {
- if (null == user) {
+ if (null == _user) {
try {
- user = Users.getUser(_login);
+ _user = Users.getUser(_login);
+ _logger.debug("Retrieved user with login {}", _login);
} catch (UserInitException e) {
throw new NrgServiceRuntimeException(NrgServiceError.UserServiceError, "User object for name " + _login + " could not be initialized.");
} catch (UserNotFoundException e) {
throw new NrgServiceRuntimeException(NrgServiceError.UserNotFoundError, "User with name " + _login + " could not be found.");
}
}
- return user;
+ return _user;
}
/**
@@ -57,7 +60,20 @@ public class XnatUserProvider implements Provider<UserI> {
return _login;
}
+ /**
+ * Sets the configured login name for the default user.
+ *
+ * @param login The user login name to configure.
+ */
+ public void setLogin(final String login) {
+ if (!StringUtils.equals(_login, login)) {
+ _login = login;
+ _user = null;
+ }
+ }
+
private final Logger _logger = LoggerFactory.getLogger(XnatUserProvider.class);
- private final String _login;
- private UserI user = null;
+
+ private String _login;
+ private UserI _user = null;
}
diff --git a/src/main/resources/META-INF/xnat/preferences/site-config.properties b/src/main/resources/META-INF/xnat/preferences/site-config.properties
deleted file mode 100644
index 0539c38c5d9019b4c5c665ffa01c69851b7aa52e..0000000000000000000000000000000000000000
--- a/src/main/resources/META-INF/xnat/preferences/site-config.properties
+++ /dev/null
@@ -1,62 +0,0 @@
-#
-# web: site-config.properties
-# XNAT http://www.xnat.org
-# Copyright (c) 2016, Washington University School of Medicine and Howard Hughes Medical Institute
-# All Rights Reserved
-#
-# Released under the Simplified BSD.
-#
-
-# The XNAT siteConfiguration.properties is only used as the default site-wide configuration when a
-# configuration is not already stored in the configuration service. After system initialization, the
-# contents of this file can be used to add new properties to the system, but not to change the values
-# of existing properties. For that, you should only modify site properties using the standard administrative
-# interface.
-checksums=true
-#checksums.property.changed.listener=org.nrg.xnat.utils.ChecksumsSiteConfigurationListener
-#showapplet=false
-enableDicomReceiver=true
-enableDicomReceiver.property.changed.listener=org.nrg.dcm.DicomSCPSiteConfigurationListener
-emailVerification=true
-enableProjectAppletScript=false
-displayNameForGenericImageSession.singular=Session
-displayNameForGenericImageSession.plural=Sessions
-UI.debug-extension-points=false
-UI.allow-advanced-search=true
-UI.allow-new-user-comments=true
-UI.allow-scan-addition=true
-UI.show-left-bar=true
-UI.show-left-bar-projects=true
-UI.show-left-bar-favorites=true
-UI.show-left-bar-search=true
-UI.show-left-bar-browse=true
-UI.show-manage-files=true
-UI.allow-non-admin-project-creation=true
-UI.login_failure_message=Your login attempt failed because the username and password combination you provided was invalid or your user already has the maximum number of user sessions open. After %d failed login attempts, your user account will be locked. If you believe your account is currently locked, you can:<ul><li>Unlock it by resetting your password</li><li>Wait one hour for it to unlock automatically</li></ul>
-
-# Indicates whether access to the list of system users should be restricted to site administrators only.
-restrictUserListAccessToAdmins=false
-
-UI.allow-blocked-subject-assessor-view=false
-
-files.zip_extensions=zip,jar,rar,ear,gar,mrb
-
-emailAllowNonuserSubscribers=true
-
-requireSaltedPasswords=false
-
-siteDescriptionType=Page
-siteDescriptionPage=/screens/site_description.vm
-siteDescriptionText=SITE DESCRIPTION HERE: Go to Administer -> Configuration -> Site Information to change.
-siteLoginLanding=/screens/QuickSearch.vm
-siteLandingLayout=/Index.vm
-siteHome=/screens/QuickSearch.vm
-siteHomeLayout=/Index.vm
-
-scanTypeMapping=true
-
-passwordExpirationType=Interval
-# Interval, in days, for expiring unchanged passwords (0 disables feature). Uses PostgreSQL interval notation: http://www.postgresql.org/docs/9.0/static/functions-datetime.html
-passwordExpirationInterval=1 year
-# Date for expiring passwords. Generally null by default.
-passwordExpirationDate=
\ No newline at end of file
diff --git a/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml b/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml
index ec8e5b881b6bfc6ef39ba7f02dbe5cd7a40c249b..81c14af4009dfca4c6bc0518cc03535a814345bd 100644
--- a/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml
+++ b/src/main/resources/META-INF/xnat/spawner/site-admin-elements.yaml
@@ -308,7 +308,7 @@ generalSecuritySettings:
contents:
securityChannel:
kind: panel.select.single
- name: ":security.channel"
+ name: ":securityChannel"
label: Security Channel
options:
any: Any
@@ -332,7 +332,7 @@ generalSecuritySettings:
description: "Should this site restrict access to the list of system users to site administrators only? If turned on, the site is more secure, but this restricts project owners from being able to administer users in their projects directly."
uiAllowNonAdminProjectCreation:
kind: panel.input.switchbox
- name: ":UI.allow-non-admin-project-creation"
+ name: ":uiAllowNonAdminProjectCreation"
label: "Allow non-administrators <br>to create projects?"
onText: Allow
offText: Do Not Allow
@@ -384,17 +384,17 @@ userLoginsSessionControls:
# description: Allow user to resume where they left off, if logging back in after a session timeout?
maximumConcurrentSessions:
kind: panel.input.number
- name: ":sessions.concurrent_max"
+ name: ":concurrentMaxSessions"
label: Maximum Concurrent Sessions
validation: integer gte:1 onblur
description: The maximum number of permitted sessions a user can have open simultaneously. You must restart Tomcat for changes to this to take effect.
loginFailureMessage:
kind: panel.textarea
- name: ":UI.login_failure_message"
+ name: ":uiLoginFailureMessage"
label: Login Failure Message
code: html
description: Text to show when a user fails to login
-# value: "?? XNAT:data:siteConfig:UI.login_failure_message"
+# value: "?? XNAT:data:siteConfig:uiLoginFailureMessage"
maximumFailedLogins:
kind: panel.input.number
name: maxFailedLogins
@@ -559,25 +559,25 @@ securityServices:
securityServicesFeatureDefault:
kind: panel.input.text
# id: securityServicesFeatureDefault
- name: ":security.services.feature.default"
+ name: ":featureService"
label: Feature Default
size: 50
securityServicesFeatureRepoDefault:
kind: panel.input.text
# id: securityServicesFeatureRepoDefault
- name: ":security.services.featureRepository.default"
+ name: ":featureRepositoryService"
label: Feature Repository Default
size: 50
securityServicesRoleDefault:
kind: panel.input.text
# id: securityServicesRoleDefault
- name: ":security.services.role.default"
+ name: ":roleService"
label: Role Default
size: 50
securityServicesRoleRepositoryDefault:
kind: panel.input.text
# id: securityServicesRoleRepositoryDefault
- name: ":security.services.roleRepository.default"
+ name: ":roleRepositoryService"
label: Role Repository Default
size: 50
@@ -591,33 +591,33 @@ emailServerSettings:
contents:
smtpEnabled:
kind: panel.input.switchbox
- name: ":smtp.enabled"
+ name: ":smtpEnabled"
label: "Enable SMTP?"
onText: Enabled
offText: Disabled
hostname:
kind: panel.input.text
- name: host
+ name: smtpHostname
label: Host
placeholder: localhost
port:
kind: panel.input.number
- name: port
+ name: smtpPort
label: Port
validation: allow-empty integer onblur
placeholder: 587
username:
kind: panel.input.text
- name: username
+ name: smtpUsername
label: Username
placeholder: name@host.org
password:
kind: panel.input.password
- name: password
+ name: smtpPassword
label: Password
protocol:
kind: panel.input.text
- name: protocol
+ name: smtpProtocol
label: Protocol
placeholder: smtp
# subhead breaks up panel items
@@ -627,19 +627,19 @@ emailServerSettings:
label: Properties
smtpAuth:
kind: panel.input.switchbox
- name: ":mail.smtp.auth"
+ name: ":smtpAuth"
label: SMTP Auth?
onText: Enabled
offText: Disabled
smtpStartTls:
kind: panel.input.switchbox
- name: ":mail.smtp.starttls.enable"
+ name: ":smtpStartTls"
label: Start TLS?
onText: Enabled
offText: Disabled
- smtpSSLTrust:
+ smtpSslTrust:
kind: panel.input.text
- name: ":mail.smtp.ssl.trust"
+ name: ":smtpSslTrust"
label: SSL Trust
placeholder: localhost
emailPrefix:
@@ -1000,7 +1000,7 @@ registrationOptions:
when a user registers.
uiAllowNewUserComments:
kind: panel.input.switchbox
- name: ":UI.allow-new-user-comments"
+ name: ":uiAllowNewUserComments"
label: "Allow User Comments <br>on Registration?"
onText: Allow
offText: Do Not Allow
@@ -1015,11 +1015,11 @@ manageDataTypes:
contents:
displayNameForGenericImageSessionSingular:
kind: panel.input.text
- name: ":displayNameForGenericImageSession.singular"
+ name: ":imageSessionDisplayNameSingular"
label: "Singular Display Name For Generic Image Session Singular"
displayNameForGenericImageSessionPlural:
kind: panel.input.text
- name: ":displayNameForGenericImageSession.plural"
+ name: ":imageSessionDisplayNamePlural"
label: "Plural Display Name For Generic Image Session Singular"
sessionBuilder:
@@ -1030,6 +1030,15 @@ sessionBuilder:
contentType: json
url: /xapi/siteConfig
contents:
+ receivedFileUser:
+ kind: panel.input.text
+ name: receivedFileUser
+ label: Received File User
+ validation: id-strict max-length:40 onblur
+ placeholder: User account for performing import and archiving operations
+ description: >
+ This should be the login name of an enabled and valid user. The specified user must be a site
+ administrator.
sessionXmlRebuilderRepeat:
kind: panel.input.number
name: sessionXmlRebuilderRepeat
diff --git a/src/main/webapp/WEB-INF/conf/services.properties b/src/main/webapp/WEB-INF/conf/services.properties
deleted file mode 100644
index 429b50d9c5cb5010a892341c71e723face3bb53e..0000000000000000000000000000000000000000
--- a/src/main/webapp/WEB-INF/conf/services.properties
+++ /dev/null
@@ -1,91 +0,0 @@
-#
-# D:/Development/XNAT/1.6/xnat_builder_1_6dev/plugin-resources/conf/services.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
-#
-site.title=XNAT
-
-datasource.name=xnat
-datasource.driver=org.postgresql.Driver
-datasource.url=jdbc:postgresql://localhost/xnat
-datasource.username=xnat
-datasource.password=xnat
-
-hibernate.dialect=org.hibernate.dialect.PostgreSQL9Dialect
-hibernate.hbm2ddl.auto=update
-hibernate.show_sql=false
-hibernate.cache.use_second_level_cache=true
-hibernate.cache.use_query_cache=true
-
-mailserver.host=mail.server
-mailserver.port=25
-mailserver.username=
-mailserver.password=
-mailserver.protocol=smtp
-mailserver.admin=jrherrick@wustl.edu
-mailserver.prefix=XNAT
-
-# Session XML rebuilder settings. interval is in minutes, repeat is in milliseconds.
-services.rebuilder.interval=5
-services.rebuilder.repeat=60000
-
-# Settings for the DICOM SCP Receiver. You can change the AE title and port here, as well as change the user that is
-# used for operations on received files, e.g. archiving sessions in projects with auto-archiving.
-services.dicom.scp.aetitle=XNAT
-services.dicom.scp.port=8104
-services.dicom.scp.receivedfileuser=admin
-
-# Indicate the required security channel for the server. This can be http, https, or any.
-security.channel=any
-
-# Number of failed login attempts before accounts are temporarily locked (-1 disables feature).
-security.max_failed_logins=-1
-# Number of milliseconds to lock user accounts that have exceeded the max_failed_logins count (3600000 for 1 hour, 86400000 for 24 hours).
-security.max_failed_logins_lockout_duration=86400000
-# Number of seconds of inactivity before an account is disabled (31556926 for 1 year).
-security.inactivity_before_lockout=31556926
-
-# Interval for timing out alias tokens. Uses PostgreSQL interval notation: http://www.postgresql.org/docs/9.0/static/functions-datetime.html
-security.token_timeout=2 days
-
-# Java regular expression that new passwords must match. For no complexity checks, set this to ^.*$
-security.password_complexity=^.*$
-# Message that explains the password complexity requirements. This is displayed when user chooses a new password that fails to meet them.
-security.password_complexity_message=Password is not sufficiently complex.
-
-# Number of days for which a password cannot be reused.
-security.password_history=365
-
-# The maximum number of permitted sessions a user can have open simultaneously.
-security.sessions.concurrent_max=1000
-
-# The following parameters are used to allow/force users to enter change justifications when modifying data.
-audit.require_change_justification=false
-audit.show_change_justification=false
-
-# Sets default values for the ActiveMQ configuration.
-amq.usage.temp=128mb
-amq.usage.mem=512mb
-amq.usage.store=1gb
-
-# Comma-separated list of the providers that users will be able to use to authenticate.
-provider.providers.enabled=db
-
-provider.db.name=Database
-provider.db.id=localdb
-provider.db.type=db
-
-# Add "ldap1" to the enabled provider list above and fill in the missing fields to enable LDAP authentication.
-provider.ldap1.name=LDAP
-provider.ldap1.id=ldap1
-provider.ldap1.type=ldap
-provider.ldap1.address=
-provider.ldap1.userdn=
-provider.ldap1.password=
-provider.ldap1.search.base=
-provider.ldap1.search.filter=
diff --git a/src/main/webapp/resources/samples/prefs-init.ini b/src/main/webapp/resources/samples/prefs-init.ini
new file mode 100644
index 0000000000000000000000000000000000000000..333765e7c1141af6da7ac369d9a3d6924f516901
--- /dev/null
+++ b/src/main/webapp/resources/samples/prefs-init.ini
@@ -0,0 +1,30 @@
+#
+# prefs-init.ini
+# XNAT http://www.xnat.org
+# Copyright (c) 2016, Washington University School of Medicine
+# All Rights Reserved
+#
+# Released under the Simplified BSD.
+#
+
+[siteConfig]
+siteUrl=http://xnat-centos.xnat.org
+adminEmail=jrherrick@wustl.edu
+archivePath=/data/xnat/archive
+buildPath=/data/xnat/build
+cachePath=/data/xnat/cache
+ftpPath=/data/xnat/ftp
+pipelinePath=/data/xnat/pipeline
+prearchivePath=/data/xnat/prearchive
+initialized=true
+
+[notifications]
+hostname=smtp.gmail.com
+username=foo@gmail.com
+password=password1234
+port=587
+protocol=smtp
+smtpAuth=true
+smtpStartTls=true
+
+
diff --git a/src/main/webapp/WEB-INF/conf/xnat-conf.properties b/src/main/webapp/resources/samples/xnat-conf.properties
similarity index 100%
rename from src/main/webapp/WEB-INF/conf/xnat-conf.properties
rename to src/main/webapp/resources/samples/xnat-conf.properties
diff --git a/src/main/webapp/scripts/project/settingsTabMgmt.js b/src/main/webapp/scripts/project/settingsTabMgmt.js
index c13ccc0a0a8ae819ba613f228a03374586d26408..bbc6bd69b227c76601e2b068caeb418242a3ce12 100644
--- a/src/main/webapp/scripts/project/settingsTabMgmt.js
+++ b/src/main/webapp/scripts/project/settingsTabMgmt.js
@@ -60,8 +60,8 @@ function fullConfigHandler() {
};
var data = buildSettingsUpdateRequestBody([
- 'siteId','UI.debug-extension-points', 'siteDescriptionType', 'siteDescriptionText', 'siteDescriptionPage', 'siteUrl', 'siteAdminEmail', 'siteLoginLanding', 'siteLandingLayout', 'siteHome', 'siteHomeLayout'
- , 'enableCsrfToken', 'enableCsrfEmail', 'restrictUserListAccessToAdmins', 'UI.allow-non-admin-project-creation', 'requireSaltedPasswords', 'passwordExpirationType', 'passwordExpirationInterval', 'passwordExpirationDate'
+ 'siteId','uiDebugExtensionPoints', 'siteDescriptionType', 'siteDescriptionText', 'siteDescriptionPage', 'siteUrl', 'siteAdminEmail', 'siteLoginLanding', 'siteLandingLayout', 'siteHome', 'siteHomeLayout'
+ , 'enableCsrfToken', 'enableCsrfEmail', 'restrictUserListAccessToAdmins', 'uiAllowNonAdminProjectCreation', 'requireSaltedPasswords', 'passwordExpirationType', 'passwordExpirationInterval', 'passwordExpirationDate'
, 'archivePath', 'checksums', 'prearchivePath', 'cachePath', 'ftpPath', 'buildPath', 'pipelinePath'
, 'requireLogin', 'enableNewRegistrations', 'emailVerification'
, 'error', 'issue', 'newUser', 'update', 'emailAllowNonuserSubscribers', 'smt.enabled'
diff --git a/src/main/webapp/setup/site-setup.yaml b/src/main/webapp/setup/site-setup.yaml
index ea6d480c888b846f6fdaed3e6abfeb2ac673c1f3..516b6db29fdaf85d1cf281401207a9c38ff5d957 100644
--- a/src/main/webapp/setup/site-setup.yaml
+++ b/src/main/webapp/setup/site-setup.yaml
@@ -175,31 +175,31 @@ siteSetup:
host:
kind: panel.input.text
- name: host
+ name: smtpHostname
label: Host
placeholder: localhost
validation: required
port:
kind: panel.input.number
- name: port
+ name: smtpPort
label: Port
placeholder: 25
validation: required number
username:
kind: panel.input.text
- name: username
+ name: smtpUsername
label: Username
password:
kind: panel.input.password
- name: password
+ name: smtpPassword
label: Password
protocol:
kind: panel.input.text
- name: protocol
+ name: smtpProtocol
label: Protocol
mailServerProperties:
@@ -208,21 +208,21 @@ siteSetup:
smtpAuth:
kind: panel.input.switchbox
- name: mail.smtp.auth
+ name: smtpAuth
label: SMTP Auth?
onText: Enabled
offText: Disabled
smtpStartTls:
kind: panel.input.switchbox
- name: mail.smtp.starttls.enable
+ name: smtpStartTls
label: Start TLS?
onText: Enabled
offText: Disabled
- smtpSSLTrust:
+ smtpSslTrust:
kind: panel.input.text
- name: mail.smtp.ssl.trust
+ name: smtpSslTrust
label: SSL Trust
# =========================
diff --git a/src/main/webapp/xdat-templates/layouts/Default.vm b/src/main/webapp/xdat-templates/layouts/Default.vm
index e19a81393c27a181b494a5c0915b6d310f8861d2..a1ebfd215b5b3905035728396e56eec0bedf156f 100644
--- a/src/main/webapp/xdat-templates/layouts/Default.vm
+++ b/src/main/webapp/xdat-templates/layouts/Default.vm
@@ -8,7 +8,7 @@ $navigation.setTemplate("/bodyOpen.vm")
<!-- path: xdat-templates/layouts/Default -->
$navigation.setTemplate("/DefaultTop.vm")
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.show-left-bar","true")))
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiShowLeftBarBrowse","true")))
$navigation.setTemplate("/DefaultLeft.vm")
#end
$navigation.setTemplate("/Breadcrumb.vm")
diff --git a/src/main/webapp/xdat-templates/macros/TurbineMacros.vm b/src/main/webapp/xdat-templates/macros/TurbineMacros.vm
index 221f0065299ee54b383c392cbf8b2fe53bc8db12..fd5d4c7029771611ba07541155b48149807bb5e2 100644
--- a/src/main/webapp/xdat-templates/macros/TurbineMacros.vm
+++ b/src/main/webapp/xdat-templates/macros/TurbineMacros.vm
@@ -1636,7 +1636,7 @@ $!turbineUtils.escapeJS($s)
##Used to load globally scoped VM files and inject them into parent VMs.
#macro(addGlobalCustomScreenJS $subFolder)
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.debug-extension-points","false")))document.write("<div class='extension_js'>/templates/screens/$subFolder</div>")#end
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiDebugExtensionPoints","false")))document.write("<div class='extension_js'>/templates/screens/$subFolder</div>")#end
#foreach($screenProps in $turbineUtils.getTemplates($subFolder))
#set($templateFileName=$screenProps.getProperty("path"))
#if($user.isGuest())
@@ -1655,7 +1655,7 @@ $!turbineUtils.escapeJS($s)
##Used to load VM files for specfic data-types and their extensions and inject them into parent VMs.
#macro(addCustomScreenJS $dataType $subFolder)
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.debug-extension-points","false")))document.write("<div class='extension_js'>/templates/screens/$dataType/$subFolder</div>")#end
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiDebugExtensionPoints","false")))document.write("<div class='extension_js'>/templates/screens/$dataType/$subFolder</div>")#end
#foreach($screenProps in $turbineUtils.getTemplates($dataType,$subFolder))
#set($templateFileName=$screenProps.getProperty("path"))
#if($user.isGuest())
@@ -1674,7 +1674,7 @@ $!turbineUtils.escapeJS($s)
##Used to load globally scoped VM files and inject them into parent VMs.
#macro(addGlobalCustomScreens $subFolder)
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.debug-extension-points","false")))<div class="extension">/templates/screens/$subFolder</div>#end
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiDebugExtensionPoints","false")))<div class="extension">/templates/screens/$subFolder</div>#end
#foreach($screenProps in $turbineUtils.getTemplates($subFolder))
#set($templateFileName=$screenProps.getProperty("path"))
#if($user.isGuest())
@@ -1693,7 +1693,7 @@ $!turbineUtils.escapeJS($s)
##Used to load VM files for specfic data-types and their extensions and inject them into parent VMs.
#macro(addCustomScreens $dataType $subFolder)
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.debug-extension-points","false")))<div class="extension">/templates/screens/$dataType/$subFolder</div>#end
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiDebugExtensionPoints","false")))<div class="extension">/templates/screens/$dataType/$subFolder</div>#end
#foreach($screenProps in $turbineUtils.getTemplates($dataType,$subFolder))
#set($templateFileName=$screenProps.getProperty("path"))
#if($user.isGuest())
diff --git a/src/main/webapp/xnat-templates/layouts/Index.vm b/src/main/webapp/xnat-templates/layouts/Index.vm
index d3f68965fca42c141abbea4b840d0aa4d894ffcf..32ca192059e05eebf2fdb117ea5cea97e54b12a4 100644
--- a/src/main/webapp/xnat-templates/layouts/Index.vm
+++ b/src/main/webapp/xnat-templates/layouts/Index.vm
@@ -9,7 +9,7 @@ $navigation.setTemplate("/bodyOpen.vm")
$navigation.setTemplate("/DefaultTop.vm")
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.show-left-bar","true")))
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiShowLeftBarBrowse","true")))
<!-- DefaultLeft -->
$navigation.setTemplate("/DefaultLeft.vm")
diff --git a/src/main/webapp/xnat-templates/navigations/HeaderIncludes.vm b/src/main/webapp/xnat-templates/navigations/HeaderIncludes.vm
index e5e68f2b5ac9e0467d4643b2afe925209f65f818..38c567895592276afae0557c3b2febb53125c664 100755
--- a/src/main/webapp/xnat-templates/navigations/HeaderIncludes.vm
+++ b/src/main/webapp/xnat-templates/navigations/HeaderIncludes.vm
@@ -89,11 +89,11 @@ $navigation.setTemplate("/BaseJS.vm")
// 'page' object is same as 'context' - easier to remember?
XNAT.data.page = XNAT.data.context;
- XNAT.app.showLeftBar = $turbineUtils.toBoolean($siteConfig.getProperty("UI.show-left-bar","true"));
- XNAT.app.showLeftBarProjects = $turbineUtils.toBoolean($siteConfig.getProperty("UI.show-left-bar-projects","true"));
- XNAT.app.showLeftBarFavorites = $turbineUtils.toBoolean($siteConfig.getProperty("UI.show-left-bar-favorites","true"));
- XNAT.app.showLeftBarSearch = $turbineUtils.toBoolean($siteConfig.getProperty("UI.show-left-bar-search","true"));
- XNAT.app.showLeftBarBrowse = $turbineUtils.toBoolean($siteConfig.getProperty("UI.show-left-bar-browse","true"));
+ XNAT.app.showLeftBar = $turbineUtils.toBoolean($siteConfig.getProperty("uiShowLeftBarBrowse","true"));
+ XNAT.app.showLeftBarProjects = $turbineUtils.toBoolean($siteConfig.getProperty("uiShowLeftBarProjects","true"));
+ XNAT.app.showLeftBarFavorites = $turbineUtils.toBoolean($siteConfig.getProperty("uiShowLeftBarFavorites","true"));
+ XNAT.app.showLeftBarSearch = $turbineUtils.toBoolean($siteConfig.getProperty("uiShowLeftBarSearch","true"));
+ XNAT.app.showLeftBarBrowse = $turbineUtils.toBoolean($siteConfig.getProperty("uiShowLeftBarBrowse","true"));
window.available_elements = [];
diff --git a/src/main/webapp/xnat-templates/navigations/XNATQuickSearch.vm b/src/main/webapp/xnat-templates/navigations/XNATQuickSearch.vm
index 41babb23fcda36252325fb0af436a9f930ab5292..7b4bb5e86829b2d3923f40508ec56f61ac0668c4 100755
--- a/src/main/webapp/xnat-templates/navigations/XNATQuickSearch.vm
+++ b/src/main/webapp/xnat-templates/navigations/XNATQuickSearch.vm
@@ -42,7 +42,7 @@ function submitQuickSearch(){
</select>
<input id="searchValue" class="clean" name="searchValue" type="text" maxlength="40" size="20" value="$!field"/>
<button type="button" id="search_btn" class="btn2" onclick="submitQuickSearch();">Go</button>
-#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-advanced-search","true")))
+#if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowAdvancedSearch","true")))
<script>
diff --git a/src/main/webapp/xnat-templates/screens/xnat_ctSessionData/edit/scans.vm b/src/main/webapp/xnat-templates/screens/xnat_ctSessionData/edit/scans.vm
index 7e2e552f5739d7774427f4b7f4f9521c8eb7e741..9b9768c8d77efb1af0c9e1c6558bb0f6b3f4a598 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_ctSessionData/edit/scans.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_ctSessionData/edit/scans.vm
@@ -5,7 +5,7 @@
#* @vtlvariable name="om" type="org.nrg.xdat.om.XnatCtsessiondata" *#
#* @vtlvariable name="scan" type="org.nrg.xdat.om.XnatImagescandata" *#
<!-- BEGIN /xnat-templates/screens/xnat_ctSessionData/edit/scans.vm -->
-#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+#if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
<DIV class="edit_header1" style="margin-bottom:16px">Scans
<input type="button" value="Add Scan" onclick="addScan(this)"/>
</DIV>
@@ -112,7 +112,7 @@
});
-#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+#if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
if(window.scanSet.scans.length==0){
for(var newC=0;newC<5;newC++){
diff --git a/src/main/webapp/xnat-templates/screens/xnat_experimentData/actionsBox/ManageFiles.vm b/src/main/webapp/xnat-templates/screens/xnat_experimentData/actionsBox/ManageFiles.vm
index c3b4e3314981dec0167bd32f42e602a781c86b4d..dc6f1c4b31df9f6285f1b2ee60cacca6ad6284b8 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_experimentData/actionsBox/ManageFiles.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_experimentData/actionsBox/ManageFiles.vm
@@ -1,5 +1,5 @@
<!-- Sequence: 5 -->
-#if($user.checkFeature($om,"manage_files") && $turbineUtils.toBoolean($siteConfig.getProperty("UI.show-manage-files","true")))
+#if($user.checkFeature($om,"manage_files") && $turbineUtils.toBoolean($siteConfig.getProperty("uiShowManageFiles","true")))
<li class="yuimenuitem">
<A href="" ONCLICK="showFiles();return false;"><div class="ic">#if($actionObject.hasImage())<img border="0" src="$content.getURI("scripts/yui/build/treeview/assets/img/folders/cf.gif")"/>#else #end</div><div class="ic_spacer"> </div>Manage Files</A>
</li>
diff --git a/src/main/webapp/xnat-templates/screens/xnat_imageSessionData/edit/scans.vm b/src/main/webapp/xnat-templates/screens/xnat_imageSessionData/edit/scans.vm
index 88cbb22a7b5fb4fa2a69255f2618439e803e3859..1f5ffacd6bcf971fc01b21ff0d37366fe25ddf42 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_imageSessionData/edit/scans.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_imageSessionData/edit/scans.vm
@@ -6,7 +6,7 @@ XNAT.app.scans={};
</script>
<DIV class="edit_header1" style="margin-bottom:16px">Scans
-#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+#if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
<input type="button" value="Add Scan" onclick="addScan(this)"/>
#end
</DIV>
@@ -113,7 +113,7 @@ XNAT.app.scans={};
});
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
if(window.scanSet.scans.length==0){
for(var newC=0;newC<5;newC++){
var tempScan = window.classMapping.newInstance(getDefaultScanXSIType());
diff --git a/src/main/webapp/xnat-templates/screens/xnat_mrSessionData/edit/scans.vm b/src/main/webapp/xnat-templates/screens/xnat_mrSessionData/edit/scans.vm
index 81bfd64b6ae52dbdfb890a7ef2e8d782ccfa49c9..360292570ffe7afb58572013103df98275b33c7a 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_mrSessionData/edit/scans.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_mrSessionData/edit/scans.vm
@@ -1,7 +1,7 @@
#* @vtlvariable name="scan" type="org.nrg.xdat.om.XnatImagescandata" *#
#* @vtlvariable name="user" type="org.nrg.xdat.security.XDATUser" *#
<!-- BEGIN /xnat-templates/screens/xnat_mrSessionData/edit/scans.vm -->
-#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+#if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
<DIV class="edit_header1" style="margin-bottom:16px">Scans
<input type="button" value="Add Scan" onclick="addScan(this)"/>
</DIV>
@@ -116,7 +116,7 @@
});
-#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+#if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
if(window.scanSet.scans.length==0){
for(var newC=0;newC<5;newC++){
diff --git a/src/main/webapp/xnat-templates/screens/xnat_petSessionData/edit/scans.vm b/src/main/webapp/xnat-templates/screens/xnat_petSessionData/edit/scans.vm
index 4e34b8168b3cb980260996272c45178329fa0de9..257f365c7211a75570db3bc347b738f9339368fe 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_petSessionData/edit/scans.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_petSessionData/edit/scans.vm
@@ -7,7 +7,7 @@
#end
<DIV class="edit_header1" style="margin-bottom:16px">Scans
-#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+#if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
<input type="button" value="Add Scan" onclick="addScan(this)"/>
#end
</DIV>
@@ -107,7 +107,7 @@
listing.render();
});
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
if(window.scanSet.scans.length==0){
for(var newC=0;newC<2;newC++){
var tempScan = window.classMapping.newInstance("xnat:petScanData");
diff --git a/src/main/webapp/xnat-templates/screens/xnat_petmrSessionData/edit/scans.vm b/src/main/webapp/xnat-templates/screens/xnat_petmrSessionData/edit/scans.vm
index 63de28f4babfbfac8b076542fe6b8e8283fbb782..4621cf1f7d6779568acc1a5c2e3451c3290af839 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_petmrSessionData/edit/scans.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_petmrSessionData/edit/scans.vm
@@ -6,7 +6,7 @@
#set($petscanTypes = $data.getSession().getAttribute("userHelper").getQueryResultsAsArrayList("select DISTINCT isd.type,isd.type from xnat_petscandata mr LEFT JOIN xnat_imagescandata isd ON mr.xnat_imagescandata_id=isd.xnat_imagescandata_id"))
#end
-#if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-scan-addition","true")))
+#if($turbineUtils.toBoolean($siteConfig.getProperty("uiAllowScanAddition","true")))
<DIV class="edit_header1" style="margin-bottom:16px">Scans
<input type="button" value="Add Scan" onclick="addScan(this)"/>
</DIV>
diff --git a/src/main/webapp/xnat-templates/screens/xnat_subjectData/actionsBox/ManageFiles.vm b/src/main/webapp/xnat-templates/screens/xnat_subjectData/actionsBox/ManageFiles.vm
index c3b4e3314981dec0167bd32f42e602a781c86b4d..dc6f1c4b31df9f6285f1b2ee60cacca6ad6284b8 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_subjectData/actionsBox/ManageFiles.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_subjectData/actionsBox/ManageFiles.vm
@@ -1,5 +1,5 @@
<!-- Sequence: 5 -->
-#if($user.checkFeature($om,"manage_files") && $turbineUtils.toBoolean($siteConfig.getProperty("UI.show-manage-files","true")))
+#if($user.checkFeature($om,"manage_files") && $turbineUtils.toBoolean($siteConfig.getProperty("uiShowManageFiles","true")))
<li class="yuimenuitem">
<A href="" ONCLICK="showFiles();return false;"><div class="ic">#if($actionObject.hasImage())<img border="0" src="$content.getURI("scripts/yui/build/treeview/assets/img/folders/cf.gif")"/>#else #end</div><div class="ic_spacer"> </div>Manage Files</A>
</li>
diff --git a/src/main/webapp/xnat-templates/screens/xnat_subjectData/xnat_subjectData_assessor.vm b/src/main/webapp/xnat-templates/screens/xnat_subjectData/xnat_subjectData_assessor.vm
index 667c20fcf99684dc968718a56cccf449615fb1e5..e8a33334014227c5bd552e4c3cf9805900bbaac5 100644
--- a/src/main/webapp/xnat-templates/screens/xnat_subjectData/xnat_subjectData_assessor.vm
+++ b/src/main/webapp/xnat-templates/screens/xnat_subjectData/xnat_subjectData_assessor.vm
@@ -2,8 +2,8 @@
##handles data that is not viewable by this user. On some servers, users can see that these exist (but not view the actual data)
##on other servers, they shouldn't see that it exists at all.
##By default, the user shouldn't see these.
-##To allow, site administrators should configure the UI.allow-blocked-subject-assessor-view peroprty in siteConfiguration.properties
- #if($turbineUtils.toBoolean($siteConfig.getProperty("UI.allow-blocked-subject-assessor-view","false")))
+##To allow, site administrators should configure the uiLoginFailureMessage peroprty in siteConfiguration.properties
+ #if($turbineUtils.toBoolean($siteConfig.getProperty("uiLoginFailureMessage","false")))
#set($denied=true)
<TR BGCOLOR="FF9999">
<TD>$!assessor.getProperty("date")</TD>