diff --git a/build.gradle b/build.gradle
index c4358a0c9775af41ce7b1ab19ce7ecc2207cfda3..7822995b9d21f0e9b7ae4d3e685a028736c83115 100644
--- a/build.gradle
+++ b/build.gradle
@@ -18,11 +18,14 @@ def vGroovy = '2.4.6'
def vJython = '2.7.0'
group 'org.nrg.xnat'
-version vXnat
buildscript {
repositories {
mavenLocal()
+ jcenter()
+ maven {
+ url "https://plugins.gradle.org/m2/"
+ }
maven {
url 'https://nrgxnat.artifactoryonline.com/nrgxnat/libs-release'
name 'XNAT Release Repository'
@@ -31,11 +34,11 @@ buildscript {
url 'https://nrgxnat.artifactoryonline.com/nrgxnat/libs-snapshot'
name 'XNAT Snapshot Repository'
}
- jcenter()
}
dependencies {
classpath "com.bmuschko:gradle-cargo-plugin:2.2.2"
classpath "com.bmuschko:gradle-tomcat-plugin:2.2.4"
+ classpath "gradle.plugin.com.zoltu.gradle.plugin:git-versioning:2.0.19"
}
}
@@ -46,6 +49,7 @@ apply plugin: 'maven'
apply plugin: 'maven-publish'
apply plugin: 'com.bmuschko.tomcat'
apply plugin: 'com.bmuschko.cargo'
+apply plugin: "com.zoltu.git-versioning"
apply plugin: 'idea'
apply plugin: 'eclipse'
@@ -135,6 +139,26 @@ if (JavaVersion.current().isJava8Compatible()) {
}
}
+// Pulls in the Jenkins BUILD_NUMBER environment variable if available.
+def buildNumber = hasProperty("BUILD_NUMBER") ? getProperty("BUILD_NUMBER") : "Manual"
+def buildDate = new Date()
+
+jar {
+ manifest {
+ attributes 'Build-Number': buildNumber,
+ 'Build-Date': buildDate,
+ 'Application-Name': 'XNAT'
+ }
+}
+
+war {
+ manifest {
+ attributes 'Build-Number': buildNumber,
+ 'Build-Date': buildDate,
+ 'Application-Name': 'XNAT'
+ }
+}
+
task sourceJar(type: Jar, dependsOn: classes) {
from sourceSets.main.allSource
}
diff --git a/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java b/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
index c912575f44b720c9d156b1c9f186a0ed0139eb9e..e88d15ba45848bc0f9db1244a01339fd0d4acdc8 100644
--- a/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
+++ b/src/main/java/org/nrg/pipeline/XnatPipelineLauncher.java
@@ -22,9 +22,7 @@ import org.nrg.xdat.om.WrkWorkflowdata;
import org.nrg.xdat.om.XnatExperimentdata;
import org.nrg.xdat.om.XnatImagesessiondata;
import org.nrg.xdat.services.AliasTokenService;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.XFT;
import org.nrg.xft.event.EventUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
@@ -54,8 +52,8 @@ public class XnatPipelineLauncher {
private UserI user;
private String dataType;
private String host;
- private Set<String> notificationEmailIds = new HashSet<String>();
- private Map<String, List<String>> parameters = new Hashtable<String, List<String>>();
+ private Set<String> notificationEmailIds = new HashSet<>();
+ private Map<String, List<String>> parameters = new Hashtable<>();
private String startAt;
private boolean waitFor;
private boolean needsBuildDir;
@@ -136,7 +134,7 @@ public class XnatPipelineLauncher {
}
if (needsBuildDir) {
- parameters.put("builddir", Arrays.asList(path));
+ parameters.put("builddir", Collections.singletonList(path));
}
setNeedsBuildDir(false);
@@ -159,7 +157,7 @@ public class XnatPipelineLauncher {
}
public XnatPipelineLauncher(RunData data, Context context) {
- user = TurbineUtils.getUser(data);
+ user = XDAT.getUserDetails();
host = TurbineUtils.GetFullServerPath();
startAt = null;
supressNotification = false;
@@ -182,7 +180,7 @@ public class XnatPipelineLauncher {
private void addUserEmailForNotification() {
notify(user.getEmail());
- notify(AdminUtils.getAdminEmailId());
+ notify(XDAT.getSiteConfigPreferences().getAdminEmail());
}
/*
@@ -192,7 +190,7 @@ public class XnatPipelineLauncher {
*/
public boolean launch() {
- return launch(XFT.GetPipelinePath() + "bin" + File.separator + SCHEDULE);
+ return launch(XDAT.getSiteConfigPreferences().getPipelinePath() + "bin" + File.separator + SCHEDULE);
}
/*
@@ -305,7 +303,7 @@ public class XnatPipelineLauncher {
command = "";
}
- command += XFT.GetPipelinePath() + "bin" + File.separator + "XnatPipelineLauncher";
+ command += XDAT.getSiteConfigPreferences().getAdminEmail() + "bin" + File.separator + "XnatPipelineLauncher";
if (System.getProperty("os.name").toUpperCase().startsWith("WINDOWS")) {
command += ".bat";
@@ -330,9 +328,9 @@ public class XnatPipelineLauncher {
* @return The pipeline configuration arguments.
*/
private List<String> getPipelineConfigurationArguments() {
- List<String> arguments = new ArrayList<String>();
+ List<String> arguments = new ArrayList<>();
try {
- String pipelinePath = new File(XFT.GetPipelinePath()).getCanonicalPath();
+ String pipelinePath = new File(XDAT.getSiteConfigPreferences().getAdminEmail()).getCanonicalPath();
boolean requiresQuotes = pipelinePath.contains(" ");
arguments.add("-config");
String configPath = pipelinePath + File.separator + "pipeline.config";
@@ -361,7 +359,7 @@ public class XnatPipelineLauncher {
private List<String> getCommandLineArguments() {
AliasToken token = XDAT.getContextService().getBean(AliasTokenService.class).issueTokenForUser(user);
- List<String> arguments = new ArrayList<String>();
+ List<String> arguments = new ArrayList<>();
arguments.add("-pipeline");
arguments.add(pipelineName);
arguments.add("-id");
@@ -437,7 +435,7 @@ public class XnatPipelineLauncher {
}
private Integer initiateWorkflowEntry() throws Exception {
- WrkWorkflowdata wrk = new WrkWorkflowdata((UserI)user);
+ WrkWorkflowdata wrk = new WrkWorkflowdata(user);
wrk.setDataType(this.getDataType());
wrk.setId(this.getId());
wrk.setExternalid(this.getExternalId());
@@ -516,7 +514,7 @@ public class XnatPipelineLauncher {
if (parameters.containsKey(name)) {
parameters.get(name).add(value);
} else {
- parameters.put(name, Arrays.asList(value));
+ parameters.put(name, Collections.singletonList(value));
}
}
@@ -528,7 +526,7 @@ public class XnatPipelineLauncher {
buildPath = buildPath.substring(0, buildPath.length() - 1);
}
if (needsBuildDir) {
- parameters.put("builddir", Arrays.asList(buildPath + File.separator + "Pipeline"));
+ parameters.put("builddir", Collections.singletonList(buildPath + File.separator + "Pipeline"));
}
}
@@ -622,11 +620,11 @@ public class XnatPipelineLauncher {
public static XnatPipelineLauncher GetLauncherForExperiment(RunData data, Context context, XnatExperimentdata imageSession) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data, context);
xnatPipelineLauncher.setSupressNotification(true);
- UserI user = TurbineUtils.getUser(data);
+ UserI user = XDAT.getUserDetails();
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
xnatPipelineLauncher.setId(imageSession.getId());
@@ -637,8 +635,8 @@ public class XnatPipelineLauncher {
xnatPipelineLauncher.setParameter("project", imageSession.getProject());
xnatPipelineLauncher.setParameter("cachepath", QCImageCreator.getQCCachePathForSession(imageSession.getProject()));
- List<String> emails = new ArrayList<String>();
- emails.add(TurbineUtils.getUser(data).getEmail());
+ List<String> emails = new ArrayList<>();
+ emails.add(XDAT.getUserDetails().getEmail());
String extraEmails = (String) TurbineUtils.GetPassedParameter("emailField", data);
if (!StringUtils.isBlank(extraEmails)) {
@@ -659,11 +657,11 @@ public class XnatPipelineLauncher {
public static XnatPipelineLauncher GetBareLauncherForExperiment(RunData data, Context context, XnatExperimentdata imageSession) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data, context);
xnatPipelineLauncher.setSupressNotification(true);
- UserI user = TurbineUtils.getUser(data);
+ UserI user = XDAT.getUserDetails();
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
xnatPipelineLauncher.setId(imageSession.getId());
diff --git a/src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java b/src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java
index 9799b168ddac98e10c72c41843ce4044cb1c0198..4165fa6172bfbf241f497af456af81c1eb0b972b 100644
--- a/src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java
+++ b/src/main/java/org/nrg/pipeline/utils/PipelineFileUtils.java
@@ -15,13 +15,14 @@ import org.apache.xmlbeans.XmlException;
import org.apache.xmlbeans.XmlObject;
import org.apache.xmlbeans.XmlOptions;
import org.nrg.pipeline.xmlbeans.PipelineDocument;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.ArcProject;
-import org.nrg.xft.XFT;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
import java.io.File;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.Calendar;
public class PipelineFileUtils {
@@ -35,7 +36,7 @@ public class PipelineFileUtils {
xopt.setErrorListener(errors);
XmlObject xo = XmlObject.Factory.parse(xmlFile, xopt);
if (errors.size() != 0) {
- throw new XmlException(errors.toArray().toString());
+ throw new XmlException(Arrays.toString(errors.toArray()));
}
//String err = XMLBeansUtils.validateAndGetErrors(xo);
//if (err != null) {
@@ -54,7 +55,7 @@ public class PipelineFileUtils {
public static String getMaxMatching(String file1, String file2, String scanId1, String scanId2) {
- String rtn = null;
+ String rtn;
if (file1 == null || file2 == null || scanId1 == null || scanId2 == null) return null;
int index = 0;
while (true) {
@@ -91,7 +92,7 @@ public class PipelineFileUtils {
public static String getBuildDir(String project, boolean postfixTimestamp) {
ArcProject arcProject = ArcSpecManager.GetFreshInstance().getProjectArc(project);
- String buildPath = XFT.GetPipelinePath() ;
+ String buildPath = XDAT.getSiteConfigPreferences().getAdminEmail() ;
if (arcProject != null) {
buildPath = arcProject.getPaths().getBuildpath();
}
diff --git a/src/main/java/org/nrg/viewer/QCImageCreator.java b/src/main/java/org/nrg/viewer/QCImageCreator.java
index fee11743b79e4e518538629459ae7aea18c27dd0..9a13829c9ff00c730f461e219d88fc999cf618df 100644
--- a/src/main/java/org/nrg/viewer/QCImageCreator.java
+++ b/src/main/java/org/nrg/viewer/QCImageCreator.java
@@ -11,24 +11,22 @@
package org.nrg.viewer;
-import java.io.File;
-
-import org.apache.log4j.Logger;
import org.nrg.pipeline.XnatPipelineLauncher;
import org.nrg.plexiViewer.lite.xml.PlexiViewerSpecForSession;
import org.nrg.plexiViewer.manager.PlexiSpecDocReader;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatMrsessiondata;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import java.io.File;
+
public class QCImageCreator {
XnatMrsessiondata mrSession;
UserI user;
- static Logger logger = Logger.getLogger(QCImageCreator.class);
-
+
public QCImageCreator(XnatMrsessiondata mrSession, UserI user) {
this.mrSession = mrSession;
this.user = user;
@@ -38,7 +36,7 @@ public class QCImageCreator {
public boolean createQCImagesForScans() throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(user);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
xnatPipelineLauncher.setWaitFor(true);
String pipelineName = "images/WebBasedQCImageCreator.xml";
@@ -53,9 +51,9 @@ public class QCImageCreator {
xnatPipelineLauncher.setParameter("session", mrSession.getId() );
xnatPipelineLauncher.setParameter("notify", "0" );
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
return xnatPipelineLauncher.launch(null);
@@ -68,8 +66,7 @@ public class QCImageCreator {
public static String GetPathToQCFile(XnatMrsessiondata mrSession, String mrScanId) {
PlexiViewerSpecForSession viewerSpec = PlexiSpecDocReader.GetInstance().getSpecDoc(mrSession.getSessionType());
- String rtn = viewerSpec.getThumbnailArchiveLocation() + File.separator + mrSession.getId() +"_" + mrScanId + "_qc.gif";
- return rtn;
+ return viewerSpec.getThumbnailArchiveLocation() + File.separator + mrSession.getId() + "_" + mrScanId + "_qc.gif";
}
@@ -79,18 +76,17 @@ public class QCImageCreator {
public static String getQCThumbnailPathForSession(String project) {
- String path = null;
+ String path;
if (project!=null){
path= ArcSpecManager.GetInstance().getCachePathForProject(project);
}else{
path= ArcSpecManager.GetInstance().getGlobalCachePath();
}
- String thumb_path = path +"Thumbnail/";
- return thumb_path;
+ return path + "Thumbnail/";
}
public static String getQCCachePathForSession(String project) {
- String path = null;
+ String path;
if (project!=null){
path= ArcSpecManager.GetInstance().getCachePathForProject(project);
}else{
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 6c3ca05a8742c8588c6e7d9eb69496c13b95a192..fcdad8eba51bb7cb3d552a1987b8575e7f119271 100644
--- a/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
+++ b/src/main/java/org/nrg/xapi/rest/settings/SiteConfigApi.java
@@ -21,11 +21,40 @@ import org.springframework.web.bind.annotation.RequestMethod;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
+import java.util.Properties;
+import java.util.jar.Attributes;
+import java.util.jar.Manifest;
@Api(description = "Site Configuration Management API")
@XapiRestController
@RequestMapping(value = "/siteConfig")
public class SiteConfigApi extends AbstractXnatRestApi {
+ @ApiOperation(value = "Returns a map of application build properties.", notes = "This includes the implementation version, Git commit hash, and build number and number.", response = Properties.class)
+ @ApiResponses({@ApiResponse(code = 200, message = "Application build properties successfully retrieved."), @ApiResponse(code = 401, message = "Must be authenticated to access the XNAT REST API."), @ApiResponse(code = 500, message = "Unexpected error")})
+ @RequestMapping(value = "buildInfo", produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
+ public ResponseEntity<Properties> getBuildInfo() {
+ if (_log.isDebugEnabled()) {
+ _log.debug("User " + getSessionUser().getUsername() + " requested the application build information.");
+ }
+
+ if (_properties.size() == 0) {
+ final Attributes attributes = _manifest.getMainAttributes();
+ _properties.setProperty("buildNumber", attributes.getValue("Build-Number"));
+ _properties.setProperty("buildDate", attributes.getValue("Build-Date"));
+ _properties.setProperty("version", attributes.getValue("Implementation-Version"));
+ _properties.setProperty("commit", attributes.getValue("Implementation-Sha"));
+ if (_log.isDebugEnabled()) {
+ _log.debug("Initialized application build information:\n * Version: {}\n * Build number: {}\n * Build Date: {}\n * Commit: {}",
+ _properties.getProperty("version"),
+ _properties.getProperty("buildNumber"),
+ _properties.getProperty("buildDate"),
+ _properties.getProperty("commit"));
+ }
+ }
+
+ return new ResponseEntity<>(_properties, HttpStatus.OK);
+ }
+
@ApiOperation(value = "Returns the full map of site configuration properties.", notes = "Complex objects may be returned as encapsulated JSON strings.", response = SiteConfigPreferences.class)
@ApiResponses({@ApiResponse(code = 200, message = "Site 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."), @ApiResponse(code = 500, message = "Unexpected error")})
@RequestMapping(produces = {MediaType.APPLICATION_JSON_VALUE}, method = {RequestMethod.GET})
@@ -134,4 +163,10 @@ public class SiteConfigApi extends AbstractXnatRestApi {
@Autowired
@Lazy
private SiteConfigPreferences _preferences;
+
+ @Autowired
+ @Lazy
+ private Manifest _manifest;
+
+ private Properties _properties = new Properties();
}
diff --git a/src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java b/src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java
index 43c0230eed9bd50b908ff3dd85fb89dd85396adc..38a16d323e25daa3b3452789bdd28251176ef865 100644
--- a/src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java
+++ b/src/main/java/org/nrg/xnat/ajax/GrantProjectAccess.java
@@ -55,7 +55,7 @@ public class GrantProjectAccess {
context.put("process","Transfer to the archive.");
context.put("system",TurbineUtils.GetSystemName());
context.put("access_level",level);
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",project);
//SEND email to user
ProjectAccessRequest.InviteUser(context, email, user, user.getFirstname() + " " + user.getLastname()
diff --git a/src/main/java/org/nrg/xnat/archive/BatchTransfer.java b/src/main/java/org/nrg/xnat/archive/BatchTransfer.java
index c28f9d3f537d00368999d3b6b793b91c03690c77..d33c56380a5ba6ff6322ed3097aee7a8182139ce 100644
--- a/src/main/java/org/nrg/xnat/archive/BatchTransfer.java
+++ b/src/main/java/org/nrg/xnat/archive/BatchTransfer.java
@@ -409,8 +409,8 @@ public class BatchTransfer extends Thread{
}
}
- String[] to = new String[] { AdminUtils.getAdminEmailId(), user.getEmail() };
- String from = AdminUtils.getAdminEmailId();
+ String[] to = new String[] { XDAT.getSiteConfigPreferences().getAdminEmail(), user.getEmail() };
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
String subject = system + " update: Archiving Complete.";
if (errors.size()>0)
subject += errors.size() + " errors";
diff --git a/src/main/java/org/nrg/xnat/archive/Transfer.java b/src/main/java/org/nrg/xnat/archive/Transfer.java
index 88dcccd9277eca735f849d4d44b1dfe3a72189ca..7fc86549ec47919711018a3fbafc55e0c636faad 100644
--- a/src/main/java/org/nrg/xnat/archive/Transfer.java
+++ b/src/main/java/org/nrg/xnat/archive/Transfer.java
@@ -20,6 +20,7 @@ import org.apache.velocity.Template;
import org.apache.velocity.VelocityContext;
import org.apache.velocity.app.Velocity;
import org.nrg.pipeline.XnatPipelineLauncher;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFT;
@@ -101,7 +102,7 @@ public class Transfer {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher((UserI)user);
// Modified by MR - 2010/03/11 AdminEmail is set in pipeline setup setup
- // xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ // xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
//Modified bt MR - 2010/03/11 There is a setting for Site Admin to set email notification for Transfer pipeline
// xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
String pipelineName = "xnat_tools/Transfer.xml";
@@ -130,10 +131,10 @@ public class Transfer {
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
xnatPipelineLauncher.setParameter("adminemail", admin_email);
xnatPipelineLauncher.setParameter("xnatserver", system);
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("sessionType", mr.getXSIType());
xnatPipelineLauncher.setParameter("xnat_project", mr.getProject());
- xnatPipelineLauncher.setParameter("logDir", XFT.GetCachePath()+"logs" + "/" + "transfer" );
+ xnatPipelineLauncher.setParameter("logDir", XDAT.getSiteConfigPreferences().getCachePath() + "logs" + "/" + "transfer");
// xnatPipelineLauncher.setParameter("notify","" +getNotifies());
xnatPipelineLauncher.setWaitFor(waitForTransfer);
diff --git a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
index 1941edcb19fe892701605e7cb800c7ab6caeb0c3..3e8b0f9124fafd14748f14380f31541b921b5ad8 100644
--- a/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
+++ b/src/main/java/org/nrg/xnat/helpers/prearchive/PrearcDatabase.java
@@ -17,6 +17,7 @@ import org.apache.commons.lang3.StringUtils;
import org.nrg.action.ClientException;
import org.nrg.automation.entities.Script;
import org.nrg.automation.services.ScriptService;
+import org.nrg.config.exceptions.ConfigServiceException;
import org.nrg.dicomtools.filters.DicomFilterService;
import org.nrg.dicomtools.filters.SeriesImportFilter;
import org.nrg.framework.constants.PrearchiveCode;
@@ -29,8 +30,9 @@ import org.nrg.xdat.bean.XnatPetmrsessiondataBean;
import org.nrg.xdat.bean.XnatPetsessiondataBean;
import org.nrg.xdat.model.XnatImagescandataI;
import org.nrg.xdat.model.XnatPetscandataI;
-import org.nrg.xdat.om.ArcArchivespecification;
import org.nrg.xdat.om.XnatExperimentdata;
+import org.nrg.xdat.preferences.InitializerSiteConfiguration;
+import org.nrg.xdat.preferences.SiteConfigPreferences;
import org.nrg.xft.db.PoolDBUtils;
import org.nrg.xft.exception.DBPoolException;
import org.nrg.xft.security.UserI;
@@ -174,10 +176,14 @@ public final class PrearcDatabase {
*/
protected static String getPrearcPath() {
- ArcArchivespecification arcSpec = ArcSpecManager.GetInstance(false);
- if (arcSpec != null) {
- return arcSpec.getGlobalPrearchivePath();
- } else {
+ final SiteConfigPreferences preferences = XDAT.getSiteConfigPreferences();
+ if (preferences != null) {
+ return preferences.getPrearchivePath();
+ }
+ try {
+ final Properties properties = XDAT.getSiteConfiguration();
+ return properties.getProperty("prearchivePath");
+ } catch (ConfigServiceException e) {
return null;
}
}
@@ -443,7 +449,7 @@ public final class PrearcDatabase {
* @return The path to the project.
*/
static String projectPath(String project) {
- return StringUtils.join(new String[]{PrearcDatabase.prearcPath, project});
+ return Paths.get(PrearcDatabase.prearcPath, project).toString();
}
/**
diff --git a/src/main/java/org/nrg/xnat/initialization/RootConfig.java b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
index 3a539cafb3ea77258db674618b10c66535386799..cb878fda7262db9a5632e5340c8cf1bd3627cde1 100644
--- a/src/main/java/org/nrg/xnat/initialization/RootConfig.java
+++ b/src/main/java/org/nrg/xnat/initialization/RootConfig.java
@@ -24,9 +24,13 @@ import org.springframework.http.converter.json.MappingJackson2HttpMessageConvert
import org.springframework.http.converter.xml.MarshallingHttpMessageConverter;
import org.springframework.oxm.jaxb.Jaxb2Marshaller;
+import javax.servlet.ServletContext;
import javax.xml.bind.Marshaller;
+import java.io.IOException;
+import java.io.InputStream;
import java.util.HashMap;
import java.util.Map;
+import java.util.jar.Manifest;
/**
* Configuration for the XNAT root application context. This contains all of the basic infrastructure for initializing
@@ -40,6 +44,13 @@ import java.util.Map;
@Import({PropertiesConfig.class, DatabaseConfig.class})
@ImportResource("WEB-INF/conf/xnat-security.xml")
public class RootConfig {
+ @Bean
+ public Manifest applicationManifest(final ServletContext context) throws IOException {
+ try (final InputStream input = context.getResourceAsStream("/META-INF/MANIFEST.MF")) {
+ return new Manifest(input);
+ }
+ }
+
@Bean
public InitializerSiteConfiguration initializerSiteConfiguration() {
return new InitializerSiteConfiguration();
diff --git a/src/main/java/org/nrg/xnat/notifications/NotifyProjectListeners.java b/src/main/java/org/nrg/xnat/notifications/NotifyProjectListeners.java
index 9a5f0b30e2cb0ae4d4bcbc070ab69f6211ed3d6c..cc1f376143c5760dba72c72d1a3c105c84f1c6ac 100644
--- a/src/main/java/org/nrg/xnat/notifications/NotifyProjectListeners.java
+++ b/src/main/java/org/nrg/xnat/notifications/NotifyProjectListeners.java
@@ -83,13 +83,13 @@ public class NotifyProjectListeners implements Callable<Boolean> {
Context context =new VelocityContext(_params);
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
context.put("user", _user);
context.put("expt", _expt);
context.put("username", _user.getUsername());
context.put("server", TurbineUtils.GetFullServerPath());
context.put("system", TurbineUtils.GetSystemName());
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("params", _params);
if(_params.get("justification")!=null){
context.put("justification",_params.get("justification"));
diff --git a/src/main/java/org/nrg/xnat/notifications/NotifyProjectPipelineListeners.java b/src/main/java/org/nrg/xnat/notifications/NotifyProjectPipelineListeners.java
index 621488d70c0a0cf8cf2d642b90b008ce7f0697a6..00ecd637de1f7f4eb4c7cb915e5d3b0713276981 100644
--- a/src/main/java/org/nrg/xnat/notifications/NotifyProjectPipelineListeners.java
+++ b/src/main/java/org/nrg/xnat/notifications/NotifyProjectPipelineListeners.java
@@ -75,21 +75,21 @@ public class NotifyProjectPipelineListeners extends NotifyProjectListeners {
email.add(e);
}
}
- if(!email.contains(AdminUtils.getAdminEmailId())){
- email.add(AdminUtils.getAdminEmailId());
+ if(!email.contains(XDAT.getSiteConfigPreferences().getAdminEmail())){
+ email.add(XDAT.getSiteConfigPreferences().getAdminEmail());
}
if(email.size()>0){
Context context =new VelocityContext(Maps.newHashMap());
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
context.put("user", _user);
context.put("expt", _expt);
context.put("username", _user.getUsername());
context.put("server", TurbineUtils.GetFullServerPath());
context.put("system", TurbineUtils.GetSystemName());
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("workflow",_workflow);
context.put("params", _params);
for(Map.Entry<String,Object> entry : _params.entrySet()) {
diff --git a/src/main/java/org/nrg/xnat/restlet/XNATApplication.java b/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
index 1bcbc4b25bf3fbaadf3d99377864e64df9f0e752..f297f018abf18274437323fc2866638744bde574 100755
--- a/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
+++ b/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
@@ -350,9 +350,6 @@ public class XNATApplication extends Application {
"/automation/templates/{TEMPLATE_ID}",
"/projects/{PROJECT_ID}/automation/templates",
"/projects/{PROJECT_ID}/automation/templates/{TEMPLATE_ID}");
- attachURI(router, "/services/settings", SettingsRestlet.class);
- attachURI(router, "/services/settings/{PROPERTY}", SettingsRestlet.class);
- attachURI(router, "/services/settings/{PROPERTY}/{VALUE}", SettingsRestlet.class);
attachURI(router, "/status/{TRANSACTION_ID}", SQListenerRepresentation.class);
@@ -401,7 +398,7 @@ public class XNATApplication extends Application {
if (clazz.isAnnotationPresent(XnatRestlet.class)) {
XnatRestlet annotation = clazz.getAnnotation(XnatRestlet.class);
final String[] urls = annotation.value();
- if (urls == null || urls.length == 0) {
+ if (urls.length == 0) {
throw new RuntimeException("The restlet extension class " + clazz.getName() + " has no URLs configured.");
}
if (annotation.secure()) {
@@ -418,7 +415,7 @@ public class XNATApplication extends Application {
}else if (clazz.isAnnotationPresent(XnatRestlet2.class)) {
XnatRestlet2 annotation = clazz.getAnnotation(XnatRestlet2.class);
final XnatRestletURI[] urls = annotation.value();
- if (urls == null || urls.length == 0) {
+ if (urls.length == 0) {
throw new RuntimeException("The restlet extension class " + clazz.getName() + " has no URLs configured.");
}
if (annotation.secure()) {
@@ -445,7 +442,7 @@ public class XNATApplication extends Application {
private void attachPath(Router router, Class<? extends Resource> clazz, XnatRestlet annotation) {
String[] paths = annotation.value();
boolean required = annotation.required();
- if (paths == null || paths.length == 0) {
+ if (paths.length == 0) {
String message = "You must specify a value for the XnatRestlet annotation to indicate the hosting path for the restlet extension in class: " + clazz.getName();
if (required) {
throw new NrgServiceRuntimeException(message);
@@ -462,7 +459,7 @@ public class XNATApplication extends Application {
private void attachPath(Router router, Class<? extends Resource> clazz, XnatRestlet2 annotation) {
XnatRestletURI[] paths = annotation.value();
boolean required = annotation.required();
- if (paths == null || paths.length == 0) {
+ if (paths.length == 0) {
String message = "You must specify a value for the XnatRestlet annotation to indicate the hosting path for the restlet extension in class: " + clazz.getName();
if (required) {
throw new NrgServiceRuntimeException(message);
@@ -477,8 +474,6 @@ public class XNATApplication extends Application {
}
private void addPublicRoutes(final Router router, List<Class<? extends Resource>> publicRoutes) {
- attachURI(router, "/version", VersionRepresentation.class);
-
if (publicRoutes == null) {
return;
}
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 4b58b4703da744f5f5c43e0a0eb0ccce081ea0c8..e0d04488f34e8e374dff1be4f69eafde8ec883d2 100644
--- a/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java
+++ b/src/main/java/org/nrg/xnat/restlet/actions/TriggerPipelines.java
@@ -10,24 +10,23 @@
*/
package org.nrg.xnat.restlet.actions;
-import java.util.concurrent.Callable;
-
import org.apache.log4j.Logger;
import org.nrg.pipeline.XnatPipelineLauncher;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatExperimentdata;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.restlet.util.XNATRestConstants;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import java.util.concurrent.Callable;
+
/**
* @author Timothy R. Olsen <olsent@wustl.edu>
*
*/
public class TriggerPipelines implements Callable<Boolean> {
- static Logger logger = Logger.getLogger(TriggerPipelines.class);
private static final String XNAT_TOOLS_AUTO_RUN_XML = "xnat_tools/AutoRun.xml";
private final XnatExperimentdata expt;
@@ -48,7 +47,7 @@ public class TriggerPipelines implements Callable<Boolean> {
public Boolean call() {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(user);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
String pipelineName = XNAT_TOOLS_AUTO_RUN_XML;
xnatPipelineLauncher.setPipelineName(pipelineName);
@@ -59,14 +58,14 @@ public class TriggerPipelines implements Callable<Boolean> {
xnatPipelineLauncher.setDataType(expt.getXSIType());
xnatPipelineLauncher.setExternalId(expt.getProject());
xnatPipelineLauncher.setWaitFor(this.waitFor);
- xnatPipelineLauncher.setParameter(XNATRestConstants.SUPRESS_EMAIL, (new Boolean(supressEmail)).toString());
+ xnatPipelineLauncher.setParameter(XNATRestConstants.SUPRESS_EMAIL, (Boolean.valueOf(supressEmail)).toString());
xnatPipelineLauncher.setParameter("session", expt.getId());
xnatPipelineLauncher.setParameter("sessionLabel", expt.getLabel());
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("sessionType", expt.getXSIType());
xnatPipelineLauncher.setParameter("xnat_project", expt.getProject());
diff --git a/src/main/java/org/nrg/xnat/restlet/extensions/AuthenticationRestlet.java b/src/main/java/org/nrg/xnat/restlet/extensions/AuthenticationRestlet.java
index cbd2dada77272f247ad4419a2e19cc80404195f6..b7f938051b9359e8e826f92eedb8486b1663e448 100644
--- a/src/main/java/org/nrg/xnat/restlet/extensions/AuthenticationRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/extensions/AuthenticationRestlet.java
@@ -14,7 +14,6 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
import org.nrg.xdat.XDAT;
-import org.nrg.xft.XFT;
import org.nrg.xnat.restlet.XnatRestlet;
import org.nrg.xnat.security.XnatProviderManager;
import org.restlet.Context;
@@ -76,7 +75,7 @@ public class AuthenticationRestlet extends Resource {
_log.debug("Passing a representation of the verify extensions restlet.");
}
- if (XFT.GetRequireLogin() && (StringUtils.isBlank(_username) || StringUtils.isBlank(_password))) {
+ if (XDAT.getSiteConfigPreferences().getRequireLogin() && (StringUtils.isBlank(_username) || StringUtils.isBlank(_password))) {
fail();
return;
}
diff --git a/src/main/java/org/nrg/xnat/restlet/guard/XnatSecureGuard.java b/src/main/java/org/nrg/xnat/restlet/guard/XnatSecureGuard.java
index 6ca69473a091f45a35c29e331ed882b1328910f7..ea38961e584bb21f4d09d90e623e87ceac47b279 100644
--- a/src/main/java/org/nrg/xnat/restlet/guard/XnatSecureGuard.java
+++ b/src/main/java/org/nrg/xnat/restlet/guard/XnatSecureGuard.java
@@ -17,7 +17,6 @@ import org.nrg.xdat.security.Authenticator;
import org.nrg.xdat.security.helpers.Users;
import org.nrg.xdat.services.AliasTokenService;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
-import org.nrg.xft.XFT;
import org.nrg.xft.security.UserI;
import org.nrg.xnat.restlet.representations.RESTLoginRepresentation;
import org.nrg.xnat.restlet.util.BrowserDetector;
@@ -114,7 +113,7 @@ public class XnatSecureGuard extends Filter {
return true;
}
}
- else if (!XFT.GetRequireLogin()) {
+ else if (!XDAT.getSiteConfigPreferences().getRequireLogin()) {
try {
HttpSession session = httpRequest.getSession();
session.removeAttribute("loggedin");
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectAccessibilityResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectAccessibilityResource.java
index 3c698e68b6b615c169aefdf095543d7d8ba5e9b3..723063c17d47d0aa80ac47341eeddbd68856ded0 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectAccessibilityResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectAccessibilityResource.java
@@ -74,19 +74,7 @@ public class ProjectAccessibilityResource extends SecureResource {
WorkflowUtils.complete(wrk, c);
}
}
-
- getResponse().setEntity(getRepresentation(getVariants().get(0)));
- Representation selectedRepresentation = getResponse().getEntity();
- if (getRequest().getConditions().hasSome()) {
- final Status status = getRequest().getConditions()
- .getStatus(getRequest().getMethod(),
- selectedRepresentation);
-
- if (status != null) {
- getResponse().setStatus(status);
- getResponse().setEntity(null);
- }
- }
+ returnDefaultRepresentation();
} catch (Exception e) {
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
}
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectGroupResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectGroupResource.java
index 87a625ec3ce5d54b2ceedb2d8a7d3d19ba8a9553..ac0b747a2cfb22ff704a3a3f621bff01595ab2e4 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectGroupResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectGroupResource.java
@@ -8,6 +8,7 @@ import java.util.Map;
import org.apache.commons.lang3.math.NumberUtils;
import org.apache.commons.lang3.StringUtils;
import org.apache.log4j.Logger;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.security.ElementSecurity;
import org.nrg.xdat.security.PermissionCriteria;
@@ -261,7 +262,7 @@ public class ProjectGroupResource extends SecureResource {
if(props.containsKey("src")){
this.getResponse().setStatus(Status.REDIRECTION_SEE_OTHER);
- this.getResponse().redirectSeeOther(XFT.GetSiteURL()+"/data/projects/"+group.getTag() + "?format=html");
+ this.getResponse().redirectSeeOther(XDAT.getSiteConfigPreferences().getSiteUrl() + "/data/projects/" + group.getTag() + "?format=html");
}else{
returnDefaultRepresentation();
}
@@ -279,7 +280,7 @@ public class ProjectGroupResource extends SecureResource {
@Override
- public Representation getRepresentation(Variant variant) {
+ public Representation represent(Variant variant) {
XFTTable table=null;
if(proj!=null){
if(group==null){
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectListResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectListResource.java
index 59122f5ca4649e27bd1096c5d90c8c3addea2f2a..17390dca051d666c6407ddb36357f83925d68563 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectListResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectListResource.java
@@ -14,6 +14,7 @@ import com.google.common.base.Joiner;
import com.google.common.collect.Lists;
import org.apache.commons.lang3.StringUtils;
import org.nrg.action.ActionException;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XdatStoredSearch;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.om.base.BaseXnatProjectdata;
@@ -25,7 +26,6 @@ import org.nrg.xdat.security.helpers.Permissions;
import org.nrg.xdat.security.helpers.Roles;
import org.nrg.xdat.security.helpers.UserHelper;
import org.nrg.xdat.security.services.UserHelperServiceI;
-import org.nrg.xft.XFT;
import org.nrg.xft.XFTItem;
import org.nrg.xft.XFTTable;
import org.nrg.xft.db.ViewManager;
@@ -56,7 +56,6 @@ public class ProjectListResource extends QueryOrganizerResource {
private static final String DATA_READABLE = "readable";
private static final String DATA_WRITABLE = "writable";
private static final List<String> PERMISSIONS = Arrays.asList(SecurityManager.ACTIVATE, SecurityManager.CREATE, SecurityManager.DELETE, SecurityManager.EDIT, SecurityManager.READ);
- private XFTTable table = null;
public ProjectListResource(Context context, Request request, Response response) {
super(context, request, response);
@@ -111,7 +110,7 @@ public class ProjectListResource extends QueryOrganizerResource {
}
if (item.getCurrentDBVersion() == null) {
- if (XFT.getBooleanProperty("UI.allow-non-admin-project-creation", true) || Roles.isSiteAdmin(user)) {
+ if (XDAT.getSiteConfigPreferences().getUiAllowNonAdminProjectCreation() || Roles.isSiteAdmin(user)) {
this.returnSuccessfulCreateFromList(BaseXnatProjectdata.createProject(project, user, allowDataDeletion, false, newEventInstance(EventUtils.CATEGORY.PROJECT_ADMIN), getQueryVariable("accessibility")));
} else {
this.getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, "User account doesn't have permission to edit this project.");
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectMemberResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectMemberResource.java
index 6bdefecc7d4ed731d33e4fbb9f7e34f4cd4a24c9..3292ce80832b1ec697418a8d851a2067503f282c 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectMemberResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectMemberResource.java
@@ -14,13 +14,14 @@ import com.noelios.restlet.ext.servlet.ServletCall;
import org.apache.commons.lang3.StringUtils;
import org.apache.velocity.VelocityContext;
import org.nrg.action.ActionException;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.display.DisplayManager;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.security.UserGroupI;
import org.nrg.xdat.security.helpers.Groups;
import org.nrg.xdat.security.helpers.Permissions;
import org.nrg.xdat.security.helpers.Users;
-import org.nrg.xdat.turbine.utils.AdminUtils;
+import org.nrg.xdat.security.user.exceptions.UserNotFoundException;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFTTable;
import org.nrg.xft.event.EventMetaI;
@@ -49,8 +50,8 @@ import java.util.List;
public class ProjectMemberResource extends SecureResource {
XnatProjectdata proj=null;
UserGroupI group=null;
- ArrayList<UserI> newUsers= new ArrayList<UserI>();
- ArrayList<String> unknown= new ArrayList<String>();
+ ArrayList<UserI> newUsers= new ArrayList<>();
+ ArrayList<String> unknown= new ArrayList<>();
String gID=null;
boolean displayHiddenUsers = false;
@@ -61,12 +62,12 @@ public class ProjectMemberResource extends SecureResource {
this.getVariants().add(new Variant(MediaType.TEXT_HTML));
this.getVariants().add(new Variant(MediaType.TEXT_XML));
- String pID= (String)getUrlEncodedParameter(request,"PROJECT_ID");
+ String pID= getUrlEncodedParameter(request, "PROJECT_ID");
if(pID!=null){
proj = XnatProjectdata.getProjectByIDorAlias(pID, user, false);
}
- gID =(String)getUrlEncodedParameter(request,"GROUP_ID");
+ gID = getUrlEncodedParameter(request, "GROUP_ID");
group=Groups.getGroup(gID);
@@ -90,44 +91,44 @@ public class ProjectMemberResource extends SecureResource {
String tempValue =(String)getParameter(request,"USER_ID");
try {
- String[] ids=null;
- if(tempValue.indexOf(",")>-1){
+ String[] ids;
+ if(tempValue.contains(",")){
ids=tempValue.split(",");
}else{
ids=new String[]{tempValue};
}
-
- for(int i=0;i<ids.length;i++){
- String uID=ids[i].trim();
- Integer xdat_user_id= null;
+
+ for (final String id : ids) {
+ String uID = id.trim();
+ Integer xdat_user_id = null;
try {
- xdat_user_id=Integer.parseInt(uID);
- } catch (NumberFormatException e) {
-
+ xdat_user_id = Integer.parseInt(uID);
+ } catch (NumberFormatException ignored) {
+
}
-
-
- if (xdat_user_id==null){
+
+
+ if (xdat_user_id == null) {
//login or email
- UserI newUser=null;
+ UserI newUser = null;
try {
newUser = Users.getUser(uID);
- } catch (Exception e) {
+ } catch (UserNotFoundException ignored) {
}
- if (newUser==null){
+ if (newUser == null) {
//by email
- List<UserI> items =Users.getUsersByEmail(uID);
- if(items.size()>0){
+ List<UserI> items = Users.getUsersByEmail(uID);
+ if (items.size() > 0) {
newUsers.addAll(items);
- }else{
+ } else {
unknown.add(uID);
}
- }else{
+ } else {
newUsers.add(newUser);
}
- }else{
+ } else {
UserI tempUser = Users.getUser(xdat_user_id);
- if (tempUser!=null){
+ if (tempUser != null) {
newUsers.add(tempUser);
}
}
@@ -167,9 +168,6 @@ public class ProjectMemberResource extends SecureResource {
}else{
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
}
- } catch (InvalidItemException e) {
- logger.error("",e);
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
} catch (Exception e) {
logger.error("",e);
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
@@ -196,7 +194,7 @@ public class ProjectMemberResource extends SecureResource {
context.put("process","Transfer to the archive.");
context.put("system",TurbineUtils.GetSystemName());
context.put("access_level",gID);
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",proj);
//SEND email to user
final PersistentWorkflowI wrk=PersistentWorkflowUtils.getOrCreateWorkflowData(null, user, XnatProjectdata.SCHEMA_ELEMENT_NAME, proj.getId(), proj.getId(), newEventInstance(EventUtils.CATEGORY.PROJECT_ACCESS, EventUtils.INVITE_USER_TO_PROJECT + " (" + uID + ")"));
@@ -224,31 +222,27 @@ public class ProjectMemberResource extends SecureResource {
for(UserI newUser: newUsers){
final PersistentWorkflowI wrk=PersistentWorkflowUtils.getOrCreateWorkflowData(null, user, Users.getUserDataType(),newUser.getID().toString(),proj.getId(),newEventInstance(EventUtils.CATEGORY.PROJECT_ACCESS, EventUtils.ADD_USER_TO_PROJECT));
EventMetaI c=wrk.buildEvent();
-
- try {
- proj.addGroupMember(group.getId(), newUser, user,WorkflowUtils.setStep(wrk, "Add " + newUser.getLogin()));
- WorkflowUtils.complete(wrk, c);
-
- if (sendmail){
- try {
- VelocityContext context = new VelocityContext();
-
- context.put("user",user);
- context.put("server",TurbineUtils.GetFullServerPath(request));
- context.put("process","Transfer to the archive.");
- context.put("system",TurbineUtils.GetSystemName());
- context.put("access_level","member");
- context.put("admin_email",AdminUtils.getAdminEmailId());
- context.put("projectOM",proj);
- org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newUser.getEmail(), user, TurbineUtils.GetSystemName() + " Access Granted for " + proj.getName());
- } catch (Throwable e) {
- logger.error("",e);
- }
- }
- } catch (Exception e) {
- throw e;
- }
- }
+
+ proj.addGroupMember(group.getId(), newUser, user,WorkflowUtils.setStep(wrk, "Add " + newUser.getLogin()));
+ WorkflowUtils.complete(wrk, c);
+
+ if (sendmail){
+ try {
+ VelocityContext context = new VelocityContext();
+
+ context.put("user",user);
+ context.put("server",TurbineUtils.GetFullServerPath(request));
+ context.put("process","Transfer to the archive.");
+ context.put("system",TurbineUtils.GetSystemName());
+ context.put("access_level","member");
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
+ context.put("projectOM",proj);
+ org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newUser.getEmail(), user, TurbineUtils.GetSystemName() + " Access Granted for " + proj.getName());
+ } catch (Throwable e) {
+ logger.error("",e);
+ }
+ }
+ }
}
}else{
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
@@ -268,26 +262,23 @@ public class ProjectMemberResource extends SecureResource {
}
@Override
- public Representation getRepresentation(Variant variant) {
+ public Representation represent(Variant variant) {
XFTTable table=null;
if(proj!=null){
try {
- StringBuffer query = new StringBuffer("SELECT g.id AS \"GROUP_ID\", displayname,login,firstname,lastname,email FROM xdat_userGroup g RIGHT JOIN xdat_user_Groupid map ON g.id=map.groupid RIGHT JOIN xdat_user u ON map.groups_groupid_xdat_user_xdat_user_id=u.xdat_user_id WHERE tag='").append(proj.getId()).append("' ");
+ StringBuilder query = new StringBuilder("SELECT g.id AS \"GROUP_ID\", displayname,login,firstname,lastname,email FROM xdat_userGroup g RIGHT JOIN xdat_user_Groupid map ON g.id=map.groupid RIGHT JOIN xdat_user u ON map.groups_groupid_xdat_user_xdat_user_id=u.xdat_user_id WHERE tag='").append(proj.getId()).append("' ");
if(!displayHiddenUsers){
query.append(" and enabled = 1 ");
}
query.append(" ORDER BY g.id DESC;");
table = XFTTable.Execute(query.toString(), user.getDBName(), user.getLogin());
- } catch (SQLException e) {
- logger.error("",e);
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- } catch (DBPoolException e) {
+ } catch (SQLException | DBPoolException e) {
logger.error("",e);
getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
}
}
- Hashtable<String,Object> params=new Hashtable<String,Object>();
+ Hashtable<String,Object> params=new Hashtable<>();
params.put("title", "Projects");
MediaType mt = overrideVariant(variant);
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectPipelineListResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectPipelineListResource.java
index d39440c5619a0955326a55f8cc2991b89697e070..648d4e2160dbfe6bf34ef8f660885d3b8120d628 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectPipelineListResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectPipelineListResource.java
@@ -13,6 +13,7 @@ package org.nrg.xnat.restlet.resources;
import org.nrg.pipeline.PipelineRepositoryManager;
import org.nrg.xdat.om.ArcProject;
+import org.nrg.xdat.om.PipePipelinerepository;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.security.helpers.Permissions;
import org.nrg.xft.XFTTable;
@@ -58,111 +59,87 @@ public class ProjectPipelineListResource extends SecureResource {
if (proj != null) {
String pathToPipeline = null;
String datatype = null;
- pathToPipeline = this.getQueryVariable("path");
- datatype = this.getQueryVariable("datatype");
- if (pathToPipeline != null && datatype != null) {
- pathToPipeline = pathToPipeline.trim();
- datatype=datatype.trim();
- boolean isUserAuthorized = isUserAuthorized();
- if (isUserAuthorized) {
- try {
+ pathToPipeline = this.getQueryVariable("path");
+ datatype = this.getQueryVariable("datatype");
+ if (pathToPipeline != null && datatype != null) {
+ pathToPipeline = pathToPipeline.trim();
+ datatype = datatype.trim();
+
+ boolean isUserAuthorized = false;
+ try {
+ isUserAuthorized = Permissions.canDelete(user, proj);
+ } catch (Exception e) {
+ e.printStackTrace();
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, "Encountered exception " + e.getMessage());
+ return;
+ }
+
+ if (isUserAuthorized) {
+ try {
ArcProject arcProject = ArcSpecManager.GetFreshInstance().getProjectArc(proj.getId());
boolean success = PipelineRepositoryManager.GetInstance().delete(arcProject, pathToPipeline, datatype, user);
if (!success) {
getLogger().log(getLogger().getLevel(), "Couldnt delete the pipeline " + pathToPipeline + " for the project " + proj.getId());
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, " Couldnt succesfully save Project Specification" );
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, " Couldn't successfully save Project Specification");
return;
- }else {
+ } else {
ArcSpecManager.Reset();
- getResponse().setEntity(getRepresentation(getVariants().get(0)));
- Representation selectedRepresentation = getResponse().getEntity();
- if (getRequest().getConditions().hasSome()) {
- final Status status = getRequest().getConditions()
- .getStatus(getRequest().getMethod(),
- selectedRepresentation);
-
- if (status != null) {
- getResponse().setStatus(status);
- getResponse().setEntity(null);
- }
- }
+ returnDefaultRepresentation();
//Send a 200 OK message back
//getResponse().setStatus(Status.SUCCESS_OK,"Pipeline has been removed from project " + _project.getId());
}
- }catch(Exception e) {
- e.printStackTrace();
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, "Encountered exception " + e.getMessage());
- }
- }else {
- getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, "User unauthroized to remove pipeline from project");
+ } catch (Exception e) {
+ e.printStackTrace();
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, "Encountered exception " + e.getMessage());
}
+ } else {
+ getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, "User unauthorized to remove pipeline from project");
}
- }else {
+ } else {
getResponse().setStatus(Status.CLIENT_ERROR_EXPECTATION_FAILED, "Expecting path and datatype as query parameters");
}
- }
-
-
-
-
- private boolean isUserAuthorized() {
- boolean isUserAuthorized = false;
- try {
- isUserAuthorized = Permissions.canDelete(user,proj);
- }catch(Exception e) {
- e.printStackTrace();
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
}
- return isUserAuthorized;
}
@Override
public Representation getRepresentation(Variant variant) {
- //Document xmldoc = null;
- boolean isUserAuthorized = isUserAuthorized();
- ArcProject arcProject = ArcSpecManager.GetFreshInstance().getProjectArc(proj.getId());
- String comment = "existing";
+ boolean isUserAuthorized;
+ try {
+ isUserAuthorized = Permissions.canRead(user, proj);
+ } catch (Exception e) {
+ e.printStackTrace();
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, "Encountered exception " + e.getMessage());
+ return null;
+ }
if (isUserAuthorized) {
- boolean additional=this.isQueryVariableTrue("additional");
-
- //Check to see if the Project already has an entry in the ArcSpec.
- //If yes, then return that entry. If not then construct a new ArcProject element and insert an attribute to say that it's an already existing
- //entry or not
- try {
- if (arcProject == null) { // No Project pipelines set in the archive specification
- if (additional) {
- arcProject = PipelineRepositoryManager.GetInstance().createNewArcProject(proj);
- comment = "new";
- }else {
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, "No archive spec entry for project " + proj.getId());
- }
- }else {
- if (additional) { //Return all the pipelines that are applicable to the project but not selected
- arcProject = PipelineRepositoryManager.GetInstance().getAdditionalPipelines(proj);
- comment = "additional";
- }else {
- //XFTItem hack = arcProject.getCurrentDBVersion(true);
- //arcProject.setItem(hack);
- }
- }
- //xmldoc = arcProject.toXML();
- //Comment commentNode = xmldoc.createComment(comment);
- //xmldoc.appendChild(commentNode);
- }catch(Exception e) {
- e.printStackTrace();
- getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
- }
- MediaType mt = overrideVariant(variant);
- if (mt.equals(MediaType.TEXT_XML)) {
- return representItem(arcProject.getItem(), mt, null,false, true);
- }else if (mt.equals(MediaType.APPLICATION_JSON)) {
- XFTTable table = PipelineRepositoryManager.GetInstance().toTable(arcProject);
-
- return representTable(table, mt,null);
- }else {
- return null;
+ ArcProject arcProject = ArcSpecManager.GetFreshInstance().getProjectArc(proj.getId());
+ boolean additional = this.isQueryVariableTrue("additional");
+
+ //Check to see if the Project already has an entry in the ArcSpec.
+ //If yes, then return that entry. If not then construct a new ArcProject element and insert an attribute to say that it's an already existing
+ //entry or not
+ try {
+ if (additional) {
+ PipePipelinerepository repository = PipelineRepositoryManager.GetInstance();
+ arcProject = arcProject == null ? repository.createNewArcProject(proj) : repository.getAdditionalPipelines(proj);
+ } else {
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL, "No archive spec entry for project " + proj.getId());
}
- }else {
+ } catch(Exception e) {
+ e.printStackTrace();
+ getResponse().setStatus(Status.SERVER_ERROR_INTERNAL);
+ }
+ MediaType mt = overrideVariant(variant);
+ if (mt.equals(MediaType.TEXT_XML)) {
+ return representItem(arcProject.getItem(), mt, null, false, true);
+ } else if (mt.equals(MediaType.APPLICATION_JSON)) {
+ XFTTable table = PipelineRepositoryManager.GetInstance().toTable(arcProject);
+
+ return representTable(table, mt,null);
+ } else {
+ return null;
+ }
+ } else {
getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN);
}
return null;
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/ProjectResource.java b/src/main/java/org/nrg/xnat/restlet/resources/ProjectResource.java
index 285997498b1aa4f2d12b7884f5b169fcf23e3aac..a819f9fca0d2d4ded17fb690f2d6d47a8c66c959 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjectResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjectResource.java
@@ -19,7 +19,6 @@ import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.om.base.BaseXnatProjectdata;
import org.nrg.xdat.security.helpers.Permissions;
import org.nrg.xdat.security.helpers.Roles;
-import org.nrg.xft.XFT;
import org.nrg.xft.XFTItem;
import org.nrg.xft.db.PoolDBUtils;
import org.nrg.xft.event.EventMetaI;
@@ -179,10 +178,10 @@ public class ProjectResource extends ItemResource {
} catch (NumberFormatException e) {
switch (qc) {
case "true":
- ap.setQuarantineCode(new Integer(1));
+ ap.setQuarantineCode(1);
break;
case "false":
- ap.setQuarantineCode(new Integer(0));
+ ap.setQuarantineCode(0);
break;
default:
getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST, "Prearchive code must be an integer.");
@@ -204,10 +203,10 @@ public class ProjectResource extends ItemResource {
} catch (NumberFormatException e) {
switch (qc) {
case "true":
- ap.setPrearchiveCode(new Integer(1));
+ ap.setPrearchiveCode(1);
break;
case "false":
- ap.setPrearchiveCode(new Integer(0));
+ ap.setPrearchiveCode(0);
break;
default:
getResponse().setStatus(Status.CLIENT_ERROR_BAD_REQUEST, "Prearchive code must be an integer.");
@@ -267,7 +266,7 @@ public class ProjectResource extends ItemResource {
}
}
- if (XFT.getBooleanProperty("UI.allow-non-admin-project-creation", true) || Roles.isSiteAdmin(user)) {
+ if (XDAT.getSiteConfigPreferences().getUiAllowNonAdminProjectCreation() || Roles.isSiteAdmin(user)) {
project.preSave();
BaseXnatProjectdata.createProject(project, user, allowDataDeletion, true, newEventInstance(EventUtils.CATEGORY.PROJECT_ADMIN), getQueryVariable("accessibility"));
} else {
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 f82bb483fa8daa66ce538349502ae605425c888d..7ebc5b72a3344a70966ca45f7a217eb7dc36168c 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/ProjtExptPipelineResource.java
@@ -11,14 +11,6 @@
package org.nrg.xnat.restlet.resources;
-import java.io.File;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
import org.apache.commons.lang3.StringUtils;
import org.apache.xmlbeans.XmlOptions;
import org.nrg.pipeline.XnatPipelineLauncher;
@@ -27,15 +19,11 @@ import org.nrg.pipeline.xmlbeans.ParameterData;
import org.nrg.pipeline.xmlbeans.ParameterData.Values;
import org.nrg.pipeline.xmlbeans.ParametersDocument;
import org.nrg.pipeline.xmlbeans.ParametersDocument.Parameters;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.ArcPipelinedataI;
import org.nrg.xdat.model.ArcPipelineparameterdataI;
-import org.nrg.xdat.om.ArcPipelinedata;
-import org.nrg.xdat.om.ArcProject;
-import org.nrg.xdat.om.XnatExperimentdata;
-import org.nrg.xdat.om.XnatImagesessiondata;
-import org.nrg.xdat.om.XnatProjectdata;
+import org.nrg.xdat.om.*;
import org.nrg.xdat.security.helpers.Permissions;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFTItem;
import org.nrg.xft.event.EventMetaI;
@@ -58,6 +46,10 @@ import org.restlet.resource.Representation;
import org.restlet.resource.Variant;
import org.xml.sax.SAXException;
+import java.io.File;
+import java.text.SimpleDateFormat;
+import java.util.*;
+
public class ProjtExptPipelineResource extends SecureResource {
XnatProjectdata proj=null;
XnatExperimentdata expt=null;
@@ -282,9 +274,9 @@ public class ProjtExptPipelineResource extends SecureResource {
hasParams.add("useremail");
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
hasParams.add("userfullname");
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
hasParams.add("adminemail");
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
hasParams.add("mailhost");
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
hasParams.add("xnatserver");
@@ -396,8 +388,8 @@ public class ProjtExptPipelineResource extends SecureResource {
xnatPipelineLauncher.setSupressNotification(true);
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
index d83c4ee370ccf78e620a3a79d68b74b968826b66..b4980f643d507d2b30d91c18aa6f4faa27344b50 100644
--- a/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
+++ b/src/main/java/org/nrg/xnat/restlet/resources/SecureResource.java
@@ -151,7 +151,7 @@ public abstract class SecureResource extends Resource {
// expects that the user exists in the session (either via traditional
// session or set via the XnatSecureGuard
user = XDAT.getUserDetails();
- if(user==null && !XFT.GetRequireLogin()){
+ if(user==null && !XDAT.getSiteConfigPreferences().getRequireLogin()){
try {
user = Users.getGuest();
XDAT.setUserDetails(user);
@@ -510,8 +510,8 @@ public abstract class SecureResource extends Resource {
return getRequest().getResourceRef().getPath();
}
- public void returnDefaultRepresentation() {
- getResponse().setEntity(getRepresentation(getVariants().get(0)));
+ public void returnRepresentation(Representation representation) {
+ getResponse().setEntity(representation);
Representation selectedRepresentation = getResponse().getEntity();
if (getRequest().getConditions().hasSome()) {
final Status status = getRequest().getConditions().getStatus(getRequest().getMethod(), selectedRepresentation);
@@ -523,6 +523,10 @@ public abstract class SecureResource extends Resource {
}
}
+ public void returnDefaultRepresentation() {
+ returnRepresentation(getRepresentation(getVariants().get(0)));
+ }
+
public Representation representItem(XFTItem item, MediaType mt, Hashtable<String, Object> metaFields, boolean allowDBAccess, boolean allowSchemaLocation) {
if (item != null) {
if (mt.equals(MediaType.TEXT_XML)) {
@@ -635,7 +639,7 @@ public abstract class SecureResource extends Resource {
public FileRepresentation representFile(File f, MediaType mt) {
mt = buildMediaType(mt, f.getName());
- if (mt.getName().startsWith("APPLICATION") || !XFT.getBooleanProperty("security.allow-HTML-resource-rendering", true)) {
+ if (mt.getName().startsWith("APPLICATION") || !XDAT.getSiteConfigPreferences().getAllowHtmlResourceRendering()) {
setContentDisposition(f.getName());
}
@@ -901,16 +905,7 @@ public abstract class SecureResource extends Resource {
targetRef = targetRef.substring(0, targetRef.indexOf("?"));
}
- getResponse().setEntity(new StringRepresentation(targetRef));
- Representation selectedRepresentation = getResponse().getEntity();
- if (getRequest().getConditions().hasSome()) {
- final Status status = getRequest().getConditions().getStatus(getRequest().getMethod(), selectedRepresentation);
-
- if (status != null) {
- getResponse().setStatus(status);
- getResponse().setEntity(null);
- }
- }
+ returnRepresentation(new StringRepresentation(targetRef));
}
public void returnString(String message, Status status) {
@@ -927,16 +922,7 @@ public abstract class SecureResource extends Resource {
}
public void returnXML(XFTItem item) {
- getResponse().setEntity(representItem(item, MediaType.TEXT_XML));
- Representation selectedRepresentation = getResponse().getEntity();
- if (getRequest().getConditions().hasSome()) {
- final Status status = getRequest().getConditions().getStatus(getRequest().getMethod(), selectedRepresentation);
-
- if (status != null) {
- getResponse().setStatus(status);
- getResponse().setEntity(null);
- }
- }
+ returnRepresentation(representItem(item, MediaType.TEXT_XML));
}
protected void setResponseHeader(String key, String value) {
diff --git a/src/main/java/org/nrg/xnat/restlet/resources/VersionRepresentation.java b/src/main/java/org/nrg/xnat/restlet/resources/VersionRepresentation.java
deleted file mode 100644
index 253558813c74c09748fecb16a0138c2d028f4bea..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/restlet/resources/VersionRepresentation.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * org.nrg.xnat.restlet.resources.VersionRepresentation
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 7/10/13 9:04 PM
- */
-package org.nrg.xnat.restlet.resources;
-
-import org.nrg.xnat.utils.FileUtils;
-import org.restlet.Context;
-import org.restlet.data.MediaType;
-import org.restlet.data.Request;
-import org.restlet.data.Response;
-import org.restlet.resource.Representation;
-import org.restlet.resource.Resource;
-import org.restlet.resource.StringRepresentation;
-import org.restlet.resource.Variant;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-import java.io.IOException;
-
-public class VersionRepresentation extends Resource {
- private final Logger logger = LoggerFactory.getLogger(VersionRepresentation.class);
-
- public VersionRepresentation(Context context, Request request, Response response) {
- super(context, request, response);
- this.getVariants().add(new Variant(MediaType.ALL));
- }
-
- @Override
- public Representation represent(Variant variant) {
- if (logger.isDebugEnabled()) {
- logger.debug("Getting XNAT version from the default configuration folder");
- }
- try {
- return new StringRepresentation(FileUtils.getXNATVersion());
- } catch (IOException exception) {
- return new StringRepresentation("[Error: check system logs]");
- }
- }
-}
diff --git a/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java b/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java
deleted file mode 100644
index 75477a76ee1e473a1b9e55537474b645637d44d9..0000000000000000000000000000000000000000
--- a/src/main/java/org/nrg/xnat/restlet/services/SettingsRestlet.java
+++ /dev/null
@@ -1,940 +0,0 @@
-/*
- * org.nrg.xnat.restlet.services.SettingsRestlet
- * XNAT http://www.xnat.org
- * Copyright (c) 2014, Washington University School of Medicine
- * All Rights Reserved
- *
- * Released under the Simplified BSD.
- *
- * Last modified 1/27/14 11:54 AM
- */
-package org.nrg.xnat.restlet.services;
-
-import org.apache.commons.lang3.StringUtils;
-import org.hibernate.PropertyNotFoundException;
-import org.json.JSONObject;
-import org.nrg.config.entities.Configuration;
-import org.nrg.config.exceptions.ConfigServiceException;
-import org.nrg.dicomtools.filters.*;
-import org.nrg.framework.exceptions.NrgServiceError;
-import org.nrg.framework.exceptions.NrgServiceRuntimeException;
-import org.nrg.framework.utilities.Patterns;
-import org.nrg.mail.api.NotificationType;
-import org.nrg.notify.api.CategoryScope;
-import org.nrg.notify.api.SubscriberType;
-import org.nrg.notify.entities.*;
-import org.nrg.notify.exceptions.DuplicateSubscriberException;
-import org.nrg.notify.services.NotificationService;
-import org.nrg.xdat.XDAT;
-import org.nrg.xdat.model.ArcArchivespecificationNotificationTypeI;
-import org.nrg.xdat.om.ArcArchivespecification;
-import org.nrg.xdat.om.ArcArchivespecificationNotificationType;
-import org.nrg.xdat.preferences.SiteConfigPreferences;
-import org.nrg.xdat.security.helpers.Roles;
-import org.nrg.xdat.security.helpers.Users;
-import org.nrg.xdat.turbine.utils.PopulateItem;
-import org.nrg.xft.XFT;
-import org.nrg.xft.XFTItem;
-import org.nrg.xft.event.EventUtils;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.restlet.representations.ItemXMLRepresentation;
-import org.nrg.xnat.restlet.resources.RestMockCallMapRestlet;
-import org.nrg.xnat.restlet.resources.SecureResource;
-import org.nrg.xnat.security.FilterSecurityInterceptorBeanPostProcessor;
-import org.nrg.xnat.security.XnatExpiredPasswordFilter;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
-import org.nrg.xnat.utils.BuildDirScriptRunnerOutputAdapter;
-import org.nrg.xnat.utils.XnatHttpUtils;
-import org.restlet.Context;
-import org.restlet.data.*;
-import org.restlet.resource.Representation;
-import org.restlet.resource.ResourceException;
-import org.restlet.resource.StringRepresentation;
-import org.restlet.resource.Variant;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-import org.springframework.security.web.access.intercept.FilterSecurityInterceptor;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.StringReader;
-import java.io.UnsupportedEncodingException;
-import java.net.URLDecoder;
-import java.util.*;
-import java.util.regex.Matcher;
-
-public class SettingsRestlet extends SecureResource {
-
- public SettingsRestlet(Context context, Request request, Response response) throws IOException {
- super(context, request, response);
-
- setModifiable(true);
-
- getVariants().add(new Variant(MediaType.APPLICATION_JSON));
- getVariants().add(new Variant(MediaType.TEXT_XML));
-
- _filterService = XDAT.getContextService().getBean(DicomFilterService.class);
-
- _arcSpec = ArcSpecManager.GetInstance();
- _property = (String) getRequest().getAttributes().get("PROPERTY");
-
- if (!StringUtils.isBlank(_property)) {
- if (_property.equals("initialize")) {
- if (_arcSpec != null && _arcSpec.isComplete()) {
- throw new RuntimeException("You can't initialize an already initialized system!");
- }
- } else {
- if (_arcSpec == null) {
- throw new RuntimeException("You haven't yet initialized the system, so I can't return any values!");
- }
- _value = (String) getRequest().getAttributes().get("VALUE");
- }
- } else {
- if (_arcSpec == null) {
- throw new RuntimeException("You haven't yet initialized the system, so I can't return any values!");
- }
- }
- if (!Roles.isSiteAdmin(user)) {
- response.setStatus(Status.CLIENT_ERROR_FORBIDDEN, "Only site admins can retrieve the system settings.");
- } else if (request.isEntityAvailable()) {
- convertFormDataToMap(request.getEntity().getText());
- }
- }
-
- @Override
- public Representation represent(Variant variant) throws ResourceException {
- final MediaType mediaType = overrideVariant(variant);
-
- try {
- if (StringUtils.isBlank(_property)) {
- return mediaType == MediaType.TEXT_XML ?
- new ItemXMLRepresentation(_arcSpec.getItem(), mediaType) :
- new StringRepresentation("{\"ResultSet\":{\"Result\":" + new JSONObject(getArcSpecAsMap()) + ", \"title\": \"Settings\"}}");
- } else {
- if (!getArcSpecAsMap().containsKey(_property)) {
- throw new PropertyNotFoundException(String.format("Setting '%s' was not found in the system.", _property));
- }
- Object propertyValue = getArcSpecAsMap().get(_property);
-
- if (mediaType == MediaType.TEXT_XML) {
- String xml = "<" + _property + ">" + propertyValue.toString() + "</" + _property + ">";
- return new StringRepresentation(xml, mediaType);
- } else {
- return new StringRepresentation("{\"ResultSet\":{\"Result\":" + toJson(propertyValue) + ", \"title\": \"" + _property + "\"}}");
- }
- }
- } catch (PropertyNotFoundException exception) {
- respondToException(exception, Status.CLIENT_ERROR_BAD_REQUEST);
- } catch (IOException | ConfigServiceException exception) {
- throw new NrgServiceRuntimeException(NrgServiceError.Unknown, "Something went wrong converting filters to JSON.", exception);
- }
- return null;
- }
-
- private Map<Object, Object> getArcSpecAsMap() throws IOException, ConfigServiceException {
- Map<Object, Object> settings = new HashMap<>();
-
- final SiteConfigPreferences preferences = XDAT.getContextService().getBean(SiteConfigPreferences.class);
-
- settings.putAll(XDAT.getSiteConfiguration());
- settings.put("siteId", preferences.getSiteId());
- final String siteUrl = StringUtils.isBlank(_arcSpec.getSiteUrl()) ? XnatHttpUtils.getServerRoot(getHttpServletRequest()) : _arcSpec.getSiteUrl();
- settings.put("siteUrl", siteUrl);
- settings.put("siteAdminEmail", _arcSpec.getSiteAdminEmail());
- settings.put("smtpHost", _arcSpec.getSmtpHost());
- settings.put("requireLogin", _arcSpec.getRequireLogin());
- settings.put("enableNewRegistrations", _arcSpec.getEnableNewRegistrations());
- settings.put("emailVerification", XDAT.getSiteConfigurationProperty("emailVerification"));
- settings.put("archivePath", _arcSpec.getGlobalArchivePath());
- settings.put("prearchivePath", _arcSpec.getGlobalPrearchivePath());
- settings.put("cachePath", _arcSpec.getGlobalCachePath());
- settings.put("buildPath", _arcSpec.getGlobalBuildPath());
- settings.put("ftpPath", _arcSpec.getGlobalpaths().getFtppath());
- settings.put("pipelinePath", _arcSpec.getGlobalpaths().getPipelinepath());
- // MIGRATION: This needs to go away when there's a proper DICOM SCP edit page.
- settings.put("dcmPort", 8104);
- settings.put("dcmAe", "XNAT");
- settings.put("enableCsrfToken", _arcSpec.getEnableCsrfToken());
- settings.put("error", getSubscribersForEvent(NotificationType.Error));
- settings.put("issue", getSubscribersForEvent(NotificationType.Issue));
- settings.put("newUser", getSubscribersForEvent(NotificationType.NewUser));
- settings.put("update", getSubscribersForEvent(NotificationType.Update));
- settings.put("anonScript", emptyStringIfNull(XDAT.getConfigService().getConfigContents("anon", "script")));
- settings.put("anonEnabled", Configuration.ENABLED_STRING.equals(XDAT.getConfigService().getStatus("anon", "script")));
- settings.put("tracerList", emptyStringIfNull(XDAT.getConfigService().getConfigContents("tracers", "tracers")));
- settings.put("appletScript", emptyStringIfNull(XDAT.getConfigService().getConfigContents("applet", "settings")));
- settings.put("restMockCallMap", getFormattedRestMockCallMap());
- final Map<String, String> filterAsMap = getSeriesImportFilterAsMap();
- if (filterAsMap != null && filterAsMap.size() > 0) {
- settings.putAll(filterAsMap);
- }
-
- return settings;
- }
-
- private String emptyStringIfNull(final String configContents) {
- return configContents == null ? "" : configContents;
- }
-
- private DicomFilterService getDicomFilterService() {
- return _filterService;
- }
-
- private SeriesImportFilter getSeriesImportFilter() {
- if (_seriesImportFilter == null) {
- _seriesImportFilter = getDicomFilterService().getSeriesImportFilter();
- }
- return _seriesImportFilter;
- }
-
- private Map<String, String> getSeriesImportFilterAsMap() {
- final SeriesImportFilter filter = getSeriesImportFilter();
- return filter == null ? null : filter.toQualifiedMap();
- }
-
- private String getFormattedRestMockCallMap() {
- Map<String, String> map = RestMockCallMapRestlet.getRestMockCallMap();
- if (map == null || map.size() == 0) {
- return StringUtils.EMPTY;
- }
- StringBuilder formattedMap = new StringBuilder();
- for (Map.Entry<String, String> call : map.entrySet()) {
- formattedMap.append(call.getKey()).append("|").append(call.getValue()).append("\n");
- }
- return formattedMap.toString();
- }
-
- private String getUnformattedRestMockCallMap(String raw) {
- if (StringUtils.isBlank(raw)) {
- return StringUtils.EMPTY;
- }
- BufferedReader reader = new BufferedReader(new StringReader(raw));
- Map<String, String> map = new HashMap<>();
- String line;
- try {
- while ((line = reader.readLine()) != null) {
- String[] atoms = line.split("\\|");
- map.put(atoms[0], atoms[1]);
- }
-
- return toJson(map);
- } catch (IOException ignored) {
- // We're not reading from a file, so we shouldn't encounter this.
- }
-
- return StringUtils.EMPTY;
- }
-
- // TODO: Gross.
- private static final String ADMIN_USERNAME_FOR_SUBSCRIPTION = "admin";
-
- /**
- * This returns the current subscriber or subscribers to a particular <i>site-wide</i> event. If the event doesn't
- * already exist, the event will be created with the default user set to the site administrator's email address.
- *
- * @param event The event to be created or retrieved.
- */
- private synchronized String getSubscribersForEvent(NotificationType event) {
- Category category;
- Definition definition;
-
- synchronized (_log) {
- category = getSiteEventCategory(event);
- definition = getSiteEventDefinition(category);
- }
-
- Map<Subscriber, Subscription> subscriptions = getNotificationService().getSubscriptionService().getSubscriberMapOfSubscriptionsForDefinition(definition);
- if (subscriptions != null && subscriptions.size() > 0) {
- return createCommaSeparatedList(subscriptions.keySet());
- } else {
- Subscriber adminUser = getNotificationService().getSubscriberService().getSubscriberByName(ADMIN_USERNAME_FOR_SUBSCRIPTION);
- if (adminUser == null) {
- try {
- adminUser = getNotificationService().getSubscriberService().createSubscriber(ADMIN_USERNAME_FOR_SUBSCRIPTION, _arcSpec.getSiteAdminEmail());
- } catch (DuplicateSubscriberException exception) {
- // This shouldn't happen, since we just checked for the subscriber's existence.
- }
- }
-
- getNotificationService().subscribe(adminUser, SubscriberType.User, definition, XDAT.getHtmlMailChannel());
- assert adminUser != null;
- return adminUser.getEmails();
- }
- }
-
- private synchronized Category getSiteEventCategory(NotificationType event) {
- Category category = getNotificationService().getCategoryService().getCategoryByScopeAndEvent(CategoryScope.Site, event.toString());
- if (category == null) {
- category = initializeSiteEventCategory(event);
- }
- return category;
- }
-
- private synchronized Definition getSiteEventDefinition(Category category) {
- Definition definition;
- List<Definition> definitions = getNotificationService().getDefinitionService().getDefinitionsForCategory(category);
- if (definitions == null || definitions.size() == 0) {
- definition = initializeSiteEventDefinition(category);
- } else {
- definition = definitions.get(0);
- }
- return definition;
- }
-
- private String createCommaSeparatedList(final Set<Subscriber> subscribers) {
- if (subscribers == null || subscribers.size() == 0) {
- return "";
- }
- boolean isFirst = true;
- StringBuilder buffer = new StringBuilder();
- for (Subscriber subscriber : subscribers) {
- if (isFirst) {
- isFirst = false;
- } else {
- buffer.append(", ");
- }
- buffer.append(subscriber.getEmails());
- }
- return buffer.toString();
- }
-
- @Override
- public void handlePost() {
- setProperties();
- }
-
- @Override
- public void handlePut() {
- setProperties();
- }
-
- @Override
- public void handleDelete() {
- _log.warn("Got a request to delete property with ID: " + _property + " from user: " + user.getLogin());
- returnDefaultRepresentation();
- }
-
- private void setProperties() {
- if (!Roles.isSiteAdmin(user)) {
- getResponse().setStatus(Status.CLIENT_ERROR_FORBIDDEN, "You must be an administrator to modify the site settings.");
- return;
- }
- try {
- if (!StringUtils.isBlank(_property) && !_property.equals("initialize")) {
- setDiscreteProperty();
- checkNotifications();
- returnDefaultRepresentation();
- } else if (!StringUtils.isBlank(_property)) {
- // We will only enter this if _property is "initialize", so that means we need to set up the arc spec entry.
- initializeArcSpec();
- checkNotifications();
- setPropertiesFromMap(_data);
- // Do not return a representation if we are initializing, it will attempt (and fail) to find a property called "initialize"
- } else {
- setPropertiesFromMap(_data);
- returnDefaultRepresentation();
- }
- } catch (ConfigServiceException exception) {
- throw new NrgServiceRuntimeException(NrgServiceError.Unknown, "Something went wrong retrieving site properties.", exception);
- } catch (Exception exception) {
- respondToException(exception, Status.CLIENT_ERROR_BAD_REQUEST);
- }
- }
-
- private void setPropertiesFromMap(Map<String, String> map) throws Exception {
- _log.debug("Setting arc spec property from body string: " + _form);
- boolean dirtied = false;
- boolean dirtiedNotifications = false;
- final Map<String, String> notifications = new HashMap<>();
- final Map<String, String> filter = new HashMap<>();
- for (String property : map.keySet()) {
- if (property.equals("siteId")) {
- final String siteId = map.get("siteId");
- _arcSpec.setSiteId(siteId);
- XFT.SetSiteID(siteId);
- dirtied = true;
- } else if (property.equals("siteUrl")) {
- final String siteUrl = map.get("siteUrl");
- _arcSpec.setSiteUrl(siteUrl);
- XFT.SetSiteURL(siteUrl);
- dirtied = true;
- } else if (property.equals("siteAdminEmail")) {
- final String siteAdminEmail = map.get("siteAdminEmail");
- _arcSpec.setSiteAdminEmail(siteAdminEmail);
- XFT.SetAdminEmail(siteAdminEmail);
- dirtied = true;
- } else if (property.equals("smtpHost")) {
- final String smtpHost = map.get("smtpHost");
- _arcSpec.setSmtpHost(smtpHost);
- XFT.SetAdminEmailHost(smtpHost);
- dirtied = true;
- } else if (property.equals("requireLogin")) {
- final String requireLogin = map.get("requireLogin");
- _arcSpec.setRequireLogin(requireLogin);
- XFT.SetRequireLogin(requireLogin);
- updateSecurityFilter(Boolean.parseBoolean(requireLogin));
- dirtied = true;
- } else if (property.equals("enableNewRegistrations")) {
- final String enableNewRegistrations = map.get("enableNewRegistrations");
- _arcSpec.setEnableNewRegistrations(enableNewRegistrations);
- XFT.SetUserRegistration(enableNewRegistrations);
- dirtied = true;
- } else if (property.equals("archivePath")) {
- final String archivePath = map.get("archivePath");
- _arcSpec.getGlobalpaths().setArchivepath(archivePath);
- XFT.SetArchiveRootPath(archivePath);
- dirtied = true;
- } else if (property.equals("prearchivePath")) {
- final String prearchivePath = map.get("prearchivePath");
- _arcSpec.getGlobalpaths().setPrearchivepath(prearchivePath);
- XFT.SetPrearchivePath(prearchivePath);
- dirtied = true;
- } else if (property.equals("cachePath")) {
- final String cachePath = map.get("cachePath");
- _arcSpec.getGlobalpaths().setCachepath(cachePath);
- XFT.SetCachePath(cachePath);
- dirtied = true;
- } else if (property.equals("buildPath")) {
- final String buildPath = map.get("buildPath");
- _arcSpec.getGlobalpaths().setBuildpath(buildPath);
- XFT.setBuildPath(buildPath);
- dirtied = true;
- } else if (property.equals("ftpPath")) {
- final String ftpPath = map.get("ftpPath");
- _arcSpec.getGlobalpaths().setFtppath(ftpPath);
- XFT.setFtpPath(ftpPath);
- dirtied = true;
- } else if (property.equals("pipelinePath")) {
- final String pipelinePath = map.get("pipelinePath");
- _arcSpec.getGlobalpaths().setPipelinepath(pipelinePath);
- XFT.SetPipelinePath(pipelinePath);
- dirtied = true;
- } else if (property.equals("dcmPort")) {
- _arcSpec.setDcm_dcmPort(map.get("dcmPort"));
- dirtied = true;
- } else if (property.equals("dcmAe")) {
- _arcSpec.setDcm_dcmAe(map.get("dcmAe"));
- dirtied = true;
- } else if (property.equals("enableCsrfToken")) {
- final String enableCsrfToken = map.get("enableCsrfToken");
- _arcSpec.setEnableCsrfToken(enableCsrfToken);
- XFT.SetEnableCsrfToken(enableCsrfToken);
- dirtied = true;
- } else if (property.equals("error") || property.equals("issue") || property.equals("newUser") || property.equals("update")) {
- if (!dirtiedNotifications) {
- dirtiedNotifications = true;
- clearArcSpecNotifications();
- }
- notifications.put(property, map.get(property));
- } else if (property.equals("anonScript")) {
- final String anonScript = map.get("anonScript");
- try {
- XDAT.getConfigService().replaceConfig(user.getUsername(), "Updating the site-wide anonymization script", "anon", "script", anonScript);
- } catch (ConfigServiceException exception) {
- throw new Exception("Error setting the site-wide anonymization script", exception);
- }
- dirtied = true;
- } else if (property.equals("tracerList")) {
- final String tracerList = map.get("tracerList");
- try {
- XDAT.getConfigService().replaceConfig(user.getUsername(), "Updating the site-wide list of PET tracers", "tracers", "tracers", tracerList);
- } catch (ConfigServiceException exception) {
- throw new Exception("Error setting the site-wide list of PET tracers", exception);
- }
- dirtied = true;
- } else if (property.equals("appletScript")) {
- final String appletScript = map.get("appletScript");
- try {
- XDAT.getConfigService().replaceConfig(user.getUsername(), "Updating the site-wide applet settings", "applet", "settings", appletScript);
- } catch (ConfigServiceException exception) {
- throw new Exception("Error setting the site-wide applet settings", exception);
- }
- dirtied = true;
- } else if (property.equals("restMockCallMap")) {
- final String callMap = map.get("restMockCallMap");
- try {
- XDAT.getConfigService().replaceConfig(user.getUsername(), "Updating the REST service mock call map", "rest", "mockCallMap", getUnformattedRestMockCallMap(callMap));
- } catch (ConfigServiceException exception) {
- throw new Exception("Error setting the REST service mock call map", exception);
- }
- dirtied = true;
- } else if (property.equals("enableProjectAppletScript")) {
- final String enableProjectAppletScript = map.get("enableProjectAppletScript");
- try {
- XDAT.setSiteConfigurationProperty("enableProjectAppletScript", enableProjectAppletScript);
- } catch (ConfigServiceException exception) {
- throw new Exception("Error setting the enableProjectAppletScript site info property", exception);
- }
- dirtied = true;
- } else if (property.equals("emailVerification")) {
- final String emailVerification = map.get("emailVerification");
- try {
- XDAT.setSiteConfigurationProperty("emailVerification", emailVerification);
- } catch (ConfigServiceException exception) {
- throw new Exception("Error setting the emailVerification site info property", exception);
- }
- dirtied = true;
- } else if (property.startsWith("passwordExpiration")) {
- try {
- final String current = XDAT.getSiteConfigurationProperty(property);
- final String value = map.get(property);
- if (!StringUtils.equals(current, value)) {
- dirtied = true;
- XDAT.getContextService().getBean(XnatExpiredPasswordFilter.class).setPasswordExpirationDirtied(true);
- XDAT.setSiteConfigurationProperty(property, value);
- }
- } catch (ConfigServiceException exception) {
- throw new Exception(String.format("Error getting the '%s' site info property", property), exception);
- }
- } else if (property.startsWith("seriesImportFilter")) {
- switch (property) {
- case "seriesImportFilterList":
- filter.put("contents", map.get(property).trim());
- break;
- case "seriesImportFilterMode":
- filter.put("mode", map.get(property).trim());
- break;
- case "seriesImportFilterEnabled":
- filter.put("enabled", map.get(property).trim());
- break;
- }
- } else {
- try {
- XDAT.setSiteConfigurationProperty(property, map.get(property));
- } catch (ConfigServiceException exception) {
- throw new Exception(String.format("Error setting the '%s' site info property", property), exception);
- }
- dirtied = true;
- }
- }
- if (filter.size() > 0) {
- final boolean enabled = Boolean.parseBoolean(filter.get("enabled"));
- final SeriesImportFilterMode mode = SeriesImportFilterMode.mode(filter.get("mode"));
- final SeriesImportFilter seriesImportFilter;
- if (mode == SeriesImportFilterMode.ModalityMap) {
- seriesImportFilter = new ModalityMapSeriesImportFilter(filter.get("contents"), enabled);
- } else {
- seriesImportFilter = new RegExBasedSeriesImportFilter(filter.get("contents"), mode, enabled);
- }
- if (!seriesImportFilter.equals(getSeriesImportFilter())) {
- _seriesImportFilter = null;
- getDicomFilterService().commit(seriesImportFilter, userName, "Updated site-wide series import filter from administrator UI.");
- }
- }
- if (dirtied || dirtiedNotifications) {
- if (notifications.size() > 0) {
- boolean allowNonuserSubscribers = XDAT.getBoolSiteConfigurationProperty("emailAllowNonuserSubscribers", false);
- for (Map.Entry<String, String> notification : notifications.entrySet()) {
- configureEventSubscriptions(NotificationType.valueOf(StringUtils.capitalize(notification.getKey())), notification.getValue(), allowNonuserSubscribers);
- }
- }
- ArcSpecManager.save(_arcSpec, user, newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, "Modified archive specification"));
- }
- if (map.containsKey("anonEnabled")) {
- boolean anonymize = map.get("anonEnabled").equals("true");
- boolean anonScriptCurrentlyEnabled = XDAT.getConfigService().getConfig("anon", "script").isEnabled();
- if (anonymize && !anonScriptCurrentlyEnabled) {
- try {
- XDAT.getConfigService().enable(user.getUsername(), "Enabling the site-wide anonymization script", "anon", "script");
- } catch (ConfigServiceException e) {
- e.printStackTrace();
- }
- }
- if (!anonymize && anonScriptCurrentlyEnabled) {
- try {
- XDAT.getConfigService().disable(user.getUsername(), "Disabling the site-wide anonymization script", "anon", "script");
- } catch (ConfigServiceException e) {
- e.printStackTrace();
- }
- }
- }
- }
-
- private void updateSecurityFilter(final boolean requireLogin) {
- FilterSecurityInterceptor interceptor = XDAT.getContextService().getBean(FilterSecurityInterceptor.class);
- FilterSecurityInterceptorBeanPostProcessor postProcessor = XDAT.getContextService().getBean(FilterSecurityInterceptorBeanPostProcessor.class);
- assert interceptor != null;
- assert postProcessor != null;
-
- interceptor.setSecurityMetadataSource(postProcessor.getMetadataSource(requireLogin));
- }
-
- /**
- * Sets up the subscriptions for the indicated events.
- *
- * @param notificationType The type of notification for which to configure subscriptions.
- * @param userIds The IDs of the users to be subscribed to the indicated notification.
- * @param allowNonuserSubscribers Indicates whether email addresses that are not associated with system users
- * should be allowed for subscription addresses.
- */
- private void configureEventSubscriptions(final NotificationType notificationType, final String userIds, final boolean allowNonuserSubscribers) throws Exception {
- Definition definition = retrieveSiteEventDefinition(notificationType);
- List<Subscriber> subscribers = getSubscribersFromAddresses(userIds, allowNonuserSubscribers);
- Map<Subscriber, Subscription> subscriptions = getNotificationService().getSubscriptionService().getSubscriberMapOfSubscriptionsForDefinition(definition);
- Channel channel = XDAT.getHtmlMailChannel();
-
- for (Subscriber subscriber : subscribers) {
- // If we don't have a subscription for this notification...
- if (!subscriptions.containsKey(subscriber)) {
- // Create one.
- getNotificationService().subscribe(subscriber, SubscriberType.User, definition, channel);
- // But if we do have a subscription for this notification...
- } else {
- // Remove it from the map.
- subscriptions.remove(subscriber);
- }
- }
-
- // If there are any left-over subscriptions...
- if (subscriptions.size() > 0) {
- // Those are no longer wanted (they weren't specified in the submitted list), so let's remove those subscriptions.
- for (Subscription subscription : subscriptions.values()) {
- getNotificationService().getSubscriptionService().delete(subscription);
- }
- }
-
- configureArcSpecNotificationType(_arcSpec, notificationType, subscriptions.values());
- }
-
- /**
- * @param type The type for which the definition and its associated category should be created or retrieved.
- * @return The existing or newly created definition.
- */
- private synchronized Definition retrieveSiteEventDefinition(NotificationType type) {
- Category category = getNotificationService().getCategoryService().getCategoryByScopeAndEvent(CategoryScope.Site, type.toString());
- if (category == null) {
- category = initializeSiteEventCategory(type.toString());
- }
- List<Definition> definitions = getNotificationService().getDefinitionService().getDefinitionsForCategory(category);
- Definition definition;
- if (definitions == null || definitions.size() == 0) {
- definition = initializeSiteEventDefinition(category);
- } else {
- definition = definitions.get(0);
- }
- return definition;
- }
-
- /**
- * @param event The event for which a category should be created.
- * @return The newly created category object.
- */
- private synchronized Category initializeSiteEventCategory(NotificationType event) {
- return initializeSiteEventCategory(event.toString());
- }
-
- /**
- * @param event The event for which a category should be created.
- * @return The newly created category object.
- */
- private synchronized Category initializeSiteEventCategory(String event) {
- Category category = getNotificationService().getCategoryService().newEntity();
- category.setScope(CategoryScope.Site);
- category.setEvent(event);
- getNotificationService().getCategoryService().create(category);
- return category;
- }
-
- /**
- * @param category The category for which a definition should be created.
- * @return The newly created definition object.
- */
- private synchronized Definition initializeSiteEventDefinition(Category category) {
- Definition definition = getNotificationService().getDefinitionService().newEntity();
- definition.setCategory(category);
- getNotificationService().getDefinitionService().create(definition);
- return definition;
- }
-
- /**
- * Takes a comma-separated list of "email addresses" (which actually may include {@link UserI#getEmail() email addresses},
- * {@link UserI#getLogin() XDAT user names}, and a combination of the two in the format:
- * <p/>
- * <code><i>username</i> <<i>email</i>></code>
- * <p/>
- * So for example, you may have something like this:
- * <p/>
- * <code>user1 <user1@@xnat.org>, user2, user3@xnat.org</code>
- * <p/>
- * Note that if any of the users aren't found, this method currently will have no indication other than returning fewer
- * users than are specified in the <b>emailAddresses</b> parameter.
- *
- * @param addressList The comma-separated list of usernames, email addressList, and combined IDs.
- * @param allowNonuserSubscribers Indicates whether email addresses that are not associated with system users
- * should be allowed for subscription addresses.
- * @return A list of {@link Subscriber} objects representing those users.
- */
- private List<Subscriber> getSubscribersFromAddresses(String addressList, final boolean allowNonuserSubscribers) throws Exception {
- final String[] addresses = addressList.split("[\\s]*,[\\s]*");
- if (addresses.length == 0) {
- throw new Exception("Submitted text couldn't be parsed into a list of addresses: " + addressList);
- }
-
- List<Subscriber> subscribers = new ArrayList<>();
- List<String> nonuserAddresses = new ArrayList<>();
- for (String address : addresses) {
- String username = null;
- String email = null;
- if (Patterns.USERNAME.matcher(address).matches()) {
- // Handle this as a username.
- UserI user = null;
- try {
- user = Users.getUser(address);
- } catch (Exception ignored) {
- }
- if (user != null) {
- username = address;
- email = user.getEmail();
- }
- } else if (Patterns.EMAIL.matcher(address).matches()) {
- // Handle this as an email.
- List<UserI> users = Users.getUsersByEmail(address);
- if (users != null && users.size() > 0) {
- if (users.size() == 1) {
- username = users.get(0).getLogin();
- } else {
- for (UserI user : users) {
- username = user.getLogin();
- if (Roles.isSiteAdmin(user)) {
- break;
- }
- }
- }
- email = address;
- } else if (allowNonuserSubscribers) {
- // If we allow non-user subscribers, then we'll just make the username and email address be the same.
- username = email = address;
- }
- } else {
- Matcher combinedMatcher = Patterns.COMBINED.matcher(address);
- if (combinedMatcher.matches()) {
- // Handle this as a combined. username will match first capture, email second capture (0 capture in regex is full expression).
- username = combinedMatcher.group(1);
- email = combinedMatcher.group(2);
- }
- }
-
- // If there's no username, this is a non-user address on a system that doesn't allow non-user subscribers;
- // continue so we can harvest ALL the non-user addresses, then handle them appropriately later.
- if (username == null) {
- nonuserAddresses.add(address);
- continue;
- }
-
- // If we don't have any non-user addresses, get the subscriber. If we do have any non-user addresses, we
- // have a valid user but we'll skip getting the subscriber to save ourselves the work.
- if (nonuserAddresses.size() == 0) {
- Subscriber subscriber = getNotificationService().getSubscriberService().getSubscriberByName(username);
- if (subscriber == null) {
- try {
- subscriber = getNotificationService().getSubscriberService().createSubscriber(username, email);
- } catch (DuplicateSubscriberException exception) {
- // This shouldn't happen, since we just checked for the subscriber's existence.
- }
- }
-
- assert subscriber != null;
- if (!subscriber.getEmails().equalsIgnoreCase(email)) {
- subscriber.setEmails(email);
- getNotificationService().getSubscriberService().update(subscriber);
- }
- subscribers.add(subscriber);
- }
- }
-
- if (nonuserAddresses.size() > 0) {
- throw new Exception(getBadAddressErrorMessage(nonuserAddresses));
- }
-
- return subscribers;
- }
-
- private String getBadAddressErrorMessage(final List<String> badAddresses) {
- StringBuilder buffer = new StringBuilder("<p>The following addresses were not valid usernames or emails of users of this XNAT server:</p><ul>");
- for (String address : badAddresses) {
- buffer.append("<li>").append(address).append("</li>");
- }
- buffer.append("</ul>");
- return buffer.toString();
- }
-
- private void initializeArcSpec() throws Exception {
- PopulateItem populator = new PopulateItem(copyDataToXmlPath(), user, "arc:ArchiveSpecification", true);
- XFTItem item = populator.getItem();
- item.setUser(user);
- ArcSpecManager.save(new ArcArchivespecification(item), user, newEventInstance(EventUtils.CATEGORY.SIDE_ADMIN, "Initialized archive specification"));
- _arcSpec = ArcSpecManager.GetInstance();
- BuildDirScriptRunnerOutputAdapter adapter = XDAT.getContextService().getBean(BuildDirScriptRunnerOutputAdapter.class);
- adapter.setPath(_arcSpec.getGlobalBuildPath());
- }
-
- private void setDiscreteProperty() throws Exception {
- if (getRequest().getMethod() != Method.POST) {
- if (_log.isDebugEnabled()) {
- _log.debug("Setting arc spec property: [" + _property + "] = " + _value);
- }
- if (!getArcSpecAsMap().containsKey(_property)) {
- throw new PropertyNotFoundException(String.format("Setting '%s' was not found in the system.", _property));
- }
- } else if (_log.isInfoEnabled()) {
- _log.info("Requested POST to property: [" + _property + "] = " + _value);
- }
- if (null == _value) {
- throw new NullPointerException(String.format("Setting '%s' cannot be set to NULL.", _property));
- } else {
- Map<String, String> map = new HashMap<>(1);
- map.put(_property, _value);
- setPropertiesFromMap(map);
- }
- }
-
- private Map<String, String> copyDataToXmlPath() {
- Map<String, String> data = new HashMap<>(_data.size());
- addSpecifiedProperty(data, "arc:archivespecification/site_id", "siteId");
- addSpecifiedProperty(data, "arc:archivespecification/site_url", "siteUrl");
- addSpecifiedProperty(data, "arc:archivespecification/site_admin_email", "siteAdminEmail");
- addSpecifiedProperty(data, "arc:archivespecification/smtp_host", "smtpHost");
- addSpecifiedProperty(data, "arc:archivespecification/globalpaths/archivepath", "archivePath");
- addSpecifiedProperty(data, "arc:archivespecification/globalpaths/prearchivepath", "prearchivePath");
- addSpecifiedProperty(data, "arc:archivespecification/globalpaths/cachepath", "cachePath");
- addSpecifiedProperty(data, "arc:archivespecification/globalpaths/ftppath", "ftpPath");
- addSpecifiedProperty(data, "arc:archivespecification/globalpaths/buildpath", "buildPath");
- addSpecifiedProperty(data, "arc:archivespecification/globalpaths/pipelinepath", "pipelinePath");
- addSpecifiedProperty(data, "arc:archivespecification/require_login", "requireLogin");
- addSpecifiedProperty(data, "arc:archivespecification/enable_new_registrations", "enableNewRegistrations");
- addSpecifiedProperty(data, "arc:archivespecification/dcm/dcm_ae", "dcmAe");
- addSpecifiedProperty(data, "arc:archivespecification/dcm/dcm_port", "dcmPort");
- addSpecifiedProperty(data, "arc:archivespecification/enable_csrf_token", "enableCsrfToken");
- return data;
- }
-
- /**
- * Checks whether the {@link #_data} map contains the specified key and whether the corresponding value is blank.
- * If the key exists and the value is not blank, this method puts the value into the submitted data map using the
- * submitted <b>xmlPath</b> as the key.
- *
- * @param data The data map to be populated with existing non-blank values.
- * @param xmlPath The key to use for storage in the data map.
- * @param key The key to check in the parsed data map.
- */
- private void addSpecifiedProperty(final Map<String, String> data, final String xmlPath, final String key) {
- if (_data.containsKey(key)) {
- String value = _data.get(key);
- if (!StringUtils.isBlank(value)) {
- data.put(xmlPath, value);
- }
- }
- }
-
- private void convertFormDataToMap(String text) {
- _form = text;
- _data = new HashMap<>();
- String[] entries = text.split("&");
- for (String entry : entries) {
- String[] atoms = entry.split("=", 2);
- if (atoms.length > 0) {
- if (atoms.length == 1) {
- _data.put(atoms[0], "");
- } else {
- try {
- _data.put(atoms[0], URLDecoder.decode(atoms[1], "UTF-8"));
- } catch (UnsupportedEncodingException e) {
- // This is the dumbest exception in the history of humanity: the form of this method that doesn't
- // specify an encoding is deprecated, so you have to specify an encoding. But the form of the method
- // that takes an encoding (http://bit.ly/yX56fe) has an note that emphasizes that you should only
- // use UTF-8 because "[n]ot doing so may introduce incompatibilities." Got it? You have to specify
- // it, but it should always be the same thing. Oh, and BTW? You have to catch an exception for
- // unsupported encodings because you may specify that one acceptable encoding or... something.
- //
- // I hate them.
- }
- }
- }
- }
- }
-
- /**
- * Checks whether site-side notifications exist and initializes them if not.
- *
- * @throws Exception
- */
- private void checkNotifications() throws Exception {
- // Check whether any notification types already exist and clear them if so.
- clearArcSpecNotifications();
-
- for (NotificationType type : NotificationType.values()) {
- Definition definition = retrieveSiteEventDefinition(type);
- List<Subscription> subscriptions = getNotificationService().getSubscriptionService().getSubscriptionsForDefinition(definition);
- configureArcSpecNotificationType(_arcSpec, type, subscriptions);
- }
- }
-
- private void configureArcSpecNotificationType(final ArcArchivespecification arcSpec, final NotificationType type, final Collection<Subscription> subscriptions) throws Exception {
- ArcArchivespecificationNotificationTypeI typeObj = new ArcArchivespecificationNotificationType();
- typeObj.setNotificationType(type.id());
- if (subscriptions == null || subscriptions.size() == 0) {
- typeObj.setEmailAddresses(getSiteAdminAccount(arcSpec) + " <" + arcSpec.getSiteAdminEmail() + ">");
- } else {
- StringBuilder buffer = new StringBuilder();
- boolean isFirst = true;
- for (Subscription subscription : subscriptions) {
- if (isFirst) {
- isFirst = false;
- } else {
- buffer.append(", ");
- }
- buffer.append(subscription.getSubscriber());
- }
- typeObj.setEmailAddresses(buffer.toString());
- }
- arcSpec.addNotificationTypes_notificationType(typeObj);
- }
-
- /**
- * Clears the arc spec notification listings.
- */
- private void clearArcSpecNotifications() {
- List<ArcArchivespecificationNotificationTypeI> notificationTypes;
- while ((notificationTypes = _arcSpec.getNotificationTypes_notificationType()) != null && notificationTypes.size() > 0) {
- _arcSpec.removeNotificationTypes_notificationType(0);
- }
- }
-
- /**
- * Gets the notification service instance.
- *
- * @return The notification service instance.
- */
- private NotificationService getNotificationService() {
- if (_notificationService == null) {
- _notificationService = XDAT.getNotificationService();
- }
- return _notificationService;
- }
-
- /**
- * Gets the site admin account name.
- *
- * @param arcSpec The arc spec from which the admin account can be retrieved.
- * @return The site admin account name.
- */
- private String getSiteAdminAccount(ArcArchivespecification arcSpec) {
- List<UserI> users = Users.getUsersByEmail(arcSpec.getSiteAdminEmail());
- if (users == null || users.size() == 0) {
- throw new RuntimeException("Can't find anything for the site admin email account! It must be associated with a user account: " + arcSpec.getSiteAdminEmail());
- }
- return users.get(0).getLogin();
- }
-
- private static final Logger _log = LoggerFactory.getLogger(SettingsRestlet.class);
-
- private final DicomFilterService _filterService;
-
- private NotificationService _notificationService;
- private ArcArchivespecification _arcSpec;
- private SeriesImportFilter _seriesImportFilter;
- private String _property;
- private String _value;
- private String _form;
- private Map<String, String> _data;
-}
diff --git a/src/main/java/org/nrg/xnat/restlet/services/mail/MailRestlet.java b/src/main/java/org/nrg/xnat/restlet/services/mail/MailRestlet.java
index 113758c079cfd9f9410817966113d430b0153039..b12052286a58b969040e19215d509db46e711b05 100644
--- a/src/main/java/org/nrg/xnat/restlet/services/mail/MailRestlet.java
+++ b/src/main/java/org/nrg/xnat/restlet/services/mail/MailRestlet.java
@@ -78,7 +78,7 @@ public class MailRestlet extends SecureResource {
MailMessage message = new MailMessage();
// When receiving email send requests through the REST service, the from address is always the admin, with the mail sent on behalf of the validating user.
- message.setFrom(AdminUtils.getAdminEmailId());
+ message.setFrom(XDAT.getSiteConfigPreferences().getAdminEmail());
message.setOnBehalfOf(user.getEmail());
// Handle all the addresses.
diff --git a/src/main/java/org/nrg/xnat/security/XnatInitCheckFilter.java b/src/main/java/org/nrg/xnat/security/XnatInitCheckFilter.java
index cd2826f9b4c75d8918e599d4894842864aefc73e..1960e057270a5954e951e0ea662ac613953b4f9c 100644
--- a/src/main/java/org/nrg/xnat/security/XnatInitCheckFilter.java
+++ b/src/main/java/org/nrg/xnat/security/XnatInitCheckFilter.java
@@ -10,25 +10,23 @@
*/
package org.nrg.xnat.security;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.List;
+import org.nrg.xdat.XDAT;
+import org.nrg.xdat.security.helpers.Roles;
+import org.nrg.xft.security.UserI;
+import org.nrg.xnat.utils.XnatHttpUtils;
+import org.springframework.jdbc.core.JdbcTemplate;
+import org.springframework.web.filter.GenericFilterBean;
+import javax.inject.Inject;
import javax.servlet.FilterChain;
import javax.servlet.ServletException;
import javax.servlet.ServletRequest;
import javax.servlet.ServletResponse;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
-
-import org.nrg.xdat.XDAT;
-import org.nrg.xdat.om.ArcArchivespecification;
-import org.nrg.xdat.security.helpers.Roles;
-import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.security.UserI;
-import org.nrg.xnat.turbine.utils.ArcSpecManager;
-import org.nrg.xnat.utils.XnatHttpUtils;
-import org.springframework.web.filter.GenericFilterBean;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.List;
public class XnatInitCheckFilter extends GenericFilterBean {
@@ -37,11 +35,11 @@ public class XnatInitCheckFilter extends GenericFilterBean {
final HttpServletRequest request = (HttpServletRequest) req;
final HttpServletResponse response = (HttpServletResponse) res;
- // MIGRATION: Get rid of the arcspec!!!
- final ArcArchivespecification arcSpec = ArcSpecManager.GetInstance();
-
- if (arcSpec != null && arcSpec.isComplete()) {
- //If arc spec has already been set, do not redirect.
+ // In this case, the count of siteUrl is a proxy for whether the system has been initialized.
+ @SuppressWarnings({"SqlDialectInspection", "SqlNoDataSourceInspection"})
+ final boolean initialized = _template.queryForObject("select count(*) from xhbm_preference p, xhbm_tool t where t.tool_id = 'siteConfig' and p.tool = t.id and p.name = 'siteUrl';", Integer.class) > 0;
+ if (initialized) {
+ // If the site URL has already been set, do not redirect.
chain.doFilter(req, res);
} else {
final UserI user = XDAT.getUserDetails();
@@ -50,7 +48,8 @@ public class XnatInitCheckFilter extends GenericFilterBean {
if (user == null) {
String header = request.getHeader("Authorization");
if (header != null && header.startsWith("Basic ") && !uri.contains(_initializationPath)) {
- //Users that authenticated using basic authentication receive an error message informing them that the arc spec is not set.
+ // Users that authenticated using basic authentication receive an error message informing
+ // them that the system is not yet initialized.
response.sendError(HttpServletResponse.SC_FORBIDDEN, "Site has not yet been configured.");
return;
}
@@ -66,25 +65,20 @@ public class XnatInitCheckFilter extends GenericFilterBean {
// the request is not for another page (preventing the user from navigating away from the Configuration page via the menu bar).
chain.doFilter(req, res);
} else {
- try {
- if(user == null) {
- // user not authenticated, let another filter handle the redirect
- // (NB: I tried putting this check up with the basic auth check,
- // but you get this weird redirect with 2 login pages on the same screen. Seems to work here).
- chain.doFilter(req, res);
+ if(user == null) {
+ // user not authenticated, let another filter handle the redirect
+ // (NB: I tried putting this check up with the basic auth check,
+ // but you get this weird redirect with 2 login pages on the same screen. Seems to work here).
+ chain.doFilter(req, res);
+ } else {
+ final String serverPath = XnatHttpUtils.getServerRoot(request);
+ if (Roles.isSiteAdmin(user)) {
+ //Otherwise, if the user has administrative permissions, direct the user to the configuration page.
+ response.sendRedirect(serverPath + _configurationPath);
} else {
- final String serverPath = XnatHttpUtils.getServerRoot(request);
- if (Roles.isSiteAdmin(user)) {
- //Otherwise, if the user has administrative permissions, direct the user to the configuration page.
- response.sendRedirect(serverPath + _configurationPath);
- } else {
- //The arc spec is not set but the user does not have administrative permissions. Direct the user to an error page.
- response.sendRedirect(serverPath + _nonAdminErrorPath);
- }
+ //The system is not initialized but the user does not have administrative permissions. Direct the user to an error page.
+ response.sendRedirect(serverPath + _nonAdminErrorPath);
}
- } catch (Exception e) {
- logger.error("Error checking user role in the Arc Spec Filter.", e);
- response.sendRedirect(TurbineUtils.GetFullServerPath() + _nonAdminErrorPath);
}
}
}
@@ -116,6 +110,9 @@ public class XnatInitCheckFilter extends GenericFilterBean {
return false;
}
+ @Inject
+ private JdbcTemplate _template;
+
private String _initializationPath = "";
private String _configurationPath = "";
private String _nonAdminErrorPath = "";
diff --git a/src/main/java/org/nrg/xnat/security/XnatLogoutSuccessHandler.java b/src/main/java/org/nrg/xnat/security/XnatLogoutSuccessHandler.java
index 5ec60f38e26c022e76a2897a6bc1d6e85b804b7e..4c17d3538632cf47be8777c643854be0c7b130b1 100644
--- a/src/main/java/org/nrg/xnat/security/XnatLogoutSuccessHandler.java
+++ b/src/main/java/org/nrg/xnat/security/XnatLogoutSuccessHandler.java
@@ -12,7 +12,7 @@ package org.nrg.xnat.security;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
-import org.nrg.xft.XFT;
+import org.nrg.xdat.XDAT;
import org.springframework.security.core.Authentication;
import org.springframework.security.web.authentication.AbstractAuthenticationTargetUrlRequestHandler;
import org.springframework.security.web.authentication.logout.LogoutSuccessHandler;
@@ -39,7 +39,7 @@ public class XnatLogoutSuccessHandler extends AbstractAuthenticationTargetUrlReq
}
private String getRequiredLogoutSuccessUrl() {
- final boolean requireLogin = XFT.GetRequireLogin();
+ final boolean requireLogin = XDAT.getSiteConfigPreferences().getRequireLogin();
final String returnUrl = requireLogin ? _securedXnatLogoutSuccessUrl : _openXnatLogoutSuccessUrl;
if (_log.isDebugEnabled()) {
diff --git a/src/main/java/org/nrg/xnat/services/messaging/file/MoveStoredFileRequestListener.java b/src/main/java/org/nrg/xnat/services/messaging/file/MoveStoredFileRequestListener.java
index 25cd46d5d2fcd8b633aa283305fd200c6d1c5d4a..d25ec48d401d20e035f0e236cc3ac4c57aa34452 100644
--- a/src/main/java/org/nrg/xnat/services/messaging/file/MoveStoredFileRequestListener.java
+++ b/src/main/java/org/nrg/xnat/services/messaging/file/MoveStoredFileRequestListener.java
@@ -77,7 +77,7 @@ public class MoveStoredFileRequestListener {
}
try {
- XDAT.getMailService().sendHtmlMessage(AdminUtils.getAdminEmailId(), request.getNotifyList(), subject, message);
+ XDAT.getMailService().sendHtmlMessage(XDAT.getSiteConfigPreferences().getAdminEmail(), request.getNotifyList(), subject, message);
} catch (MessagingException e) {
log.error("Failed to send email.", e);
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/AddProject.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/AddProject.java
index 6aae275a9734616b24e7a3c3da3256dc1d1e1f45..4bf7e85358218c1b6d382d2b7c0dd4f5136a8715 100755
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/AddProject.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/AddProject.java
@@ -14,16 +14,19 @@ import org.apache.commons.lang3.StringUtils;
import org.apache.turbine.modules.ScreenLoader;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.ArcProject;
import org.nrg.xdat.om.XnatProjectdata;
import org.nrg.xdat.om.base.BaseXnatProjectdata;
-import org.nrg.xdat.security.helpers.*;
+import org.nrg.xdat.security.helpers.Groups;
+import org.nrg.xdat.security.helpers.Permissions;
+import org.nrg.xdat.security.helpers.Roles;
+import org.nrg.xdat.security.helpers.UserHelper;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
import org.nrg.xdat.turbine.modules.screens.EditScreenA;
import org.nrg.xdat.turbine.utils.PopulateItem;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.ItemI;
-import org.nrg.xft.XFT;
import org.nrg.xft.XFTItem;
import org.nrg.xft.db.PoolDBUtils;
import org.nrg.xft.event.EventMetaI;
@@ -54,7 +57,7 @@ public class AddProject extends SecureAction {
context.put("tag", TurbineUtils.GetPassedParameter("tag", data));
}
- if (!XFT.getBooleanProperty("UI.allow-non-admin-project-creation", true) && !Roles.isSiteAdmin(user)) {
+ if (!XDAT.getSiteConfigPreferences().getUiAllowNonAdminProjectCreation() && !Roles.isSiteAdmin(user)) {
displayProjectEditError("Invalid permissions for this operation", data, null);
return;
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java
index 069a156e7f8428f5d0bcce02e7055198e1fe88c5..c56bcf28846779df379682f09e0e81fea9a72473 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ConfirmRegister.java
@@ -10,18 +10,18 @@
*/
package org.nrg.xnat.turbine.modules.actions;
-import java.util.List;
-
import org.apache.commons.lang3.StringUtils;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.security.helpers.Users;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
import org.nrg.xdat.turbine.modules.screens.SecureScreen;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.security.UserI;
+import java.util.List;
+
public class ConfirmRegister extends SecureAction {
@Override
@@ -38,7 +38,7 @@ public class ConfirmRegister extends SecureAction {
if(!StringUtils.isEmpty(par)){
context.put("par", par);
}
- if (!StringUtils.isEmpty(nextAction) && nextAction.indexOf("XDATLoginUser")==-1 && !nextAction.equals(org.apache.turbine.Turbine.getConfiguration().getString("action.login"))){
+ if (!StringUtils.isEmpty(nextAction) && !nextAction.contains("XDATLoginUser") && !nextAction.equals(org.apache.turbine.Turbine.getConfiguration().getString("action.login"))){
context.put("nextAction", nextAction);
}else if (!StringUtils.isEmpty(nextPage) && !nextPage.equals(org.apache.turbine.Turbine.getConfiguration().getString("template.home")) ) {
context.put("nextPage", nextPage);
@@ -50,7 +50,7 @@ public class ConfirmRegister extends SecureAction {
if (current==null)
{
//allowed to have multiple accounts with the admin email address
- if(!StringUtils.equals(newUser.getEmail(),AdminUtils.getAdminEmailId()))
+ if(!StringUtils.equals(newUser.getEmail(), XDAT.getSiteConfigPreferences().getAdminEmail()))
{
List<UserI> match=Users.getUsersByEmail(newUser.getEmail());
if(match.size()>0){
@@ -72,7 +72,7 @@ public class ConfirmRegister extends SecureAction {
data.setMessage("Username (" + newUser.getEmail() + ") already exists.");
data.setScreenTemplate("ForgotLogin.vm");
}
- } catch (Exception e) {
+ } catch (Exception ignored) {
}
}
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 aeed0589e099186e5837fbe2a633189699cb1a4e..0ac76f4e3336e9f9f513b2c4f0dde5dc2b680a8c 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
@@ -11,12 +11,6 @@
package org.nrg.xnat.turbine.modules.actions;
-import java.io.File;
-import java.text.SimpleDateFormat;
-import java.util.ArrayList;
-import java.util.Date;
-import java.util.Hashtable;
-
import org.apache.turbine.modules.ScreenLoader;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
@@ -30,17 +24,11 @@ import org.nrg.pipeline.xmlbeans.ParameterData;
import org.nrg.pipeline.xmlbeans.ParameterData.Values;
import org.nrg.pipeline.xmlbeans.ParametersDocument;
import org.nrg.pipeline.xmlbeans.ParametersDocument.Parameters;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.ArcPipelinedataI;
-import org.nrg.xdat.om.ArcProject;
-import org.nrg.xdat.om.ArcProjectDescendant;
-import org.nrg.xdat.om.ArcProjectDescendantPipeline;
-import org.nrg.xdat.om.ArcProjectPipeline;
-import org.nrg.xdat.om.PipePipelinedetails;
-import org.nrg.xdat.om.PipePipelinerepository;
-import org.nrg.xdat.om.XnatProjectdata;
+import org.nrg.xdat.om.*;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
import org.nrg.xdat.turbine.modules.screens.EditScreenA;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.PopulateItem;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFTItem;
@@ -61,6 +49,12 @@ import org.nrg.xnat.utils.WorkflowUtils;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
+import java.io.File;
+import java.text.SimpleDateFormat;
+import java.util.ArrayList;
+import java.util.Date;
+import java.util.Hashtable;
+
public class ManagePipeline extends SecureAction {
@@ -386,8 +380,8 @@ public class ManagePipeline extends SecureAction {
xnatPipelineLauncher.setSupressNotification(true);
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
xnatPipelineLauncher.setPipelineName(pipeline_path);
String exptLabel = item.getStringProperty("label");
@@ -433,7 +427,7 @@ public class ManagePipeline extends SecureAction {
for (int i = 0; i < totalParams; i++) {
String name = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("param[" + i + "].name",data));
int rowcount = TurbineUtils.GetPassedInteger("param[" + i + "].name.rowcount", data);
- ArrayList<String> formvalues = new ArrayList<String>();
+ ArrayList<String> formvalues = new ArrayList<>();
for (int j = 0; j < rowcount; j++) {
String formfieldname = "param[" + i + "][" + j + "].value";
if (TurbineUtils.HasPassedParameter(formfieldname, data)) //formvalues.add(data.getParameters().get(formfieldname));
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ManageProjectAccess.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ManageProjectAccess.java
index feba56fc7a2db917e3e7a20c8db6db6e5b900ca6..470659ef681990098851b88201e0618fa4738ac2 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ManageProjectAccess.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ManageProjectAccess.java
@@ -92,7 +92,7 @@ public class ManageProjectAccess extends SecureAction {
context.put("process", "Transfer to the archive.");
context.put("system", TurbineUtils.GetSystemName());
context.put("access_level", "owner");
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM", project);
org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newOwner, TurbineUtils.getUser(data), TurbineUtils.GetSystemName() + " Access Granted for " + project.getName());
}
@@ -126,7 +126,7 @@ public class ManageProjectAccess extends SecureAction {
context.put("process", "Transfer to the archive.");
context.put("system", TurbineUtils.GetSystemName());
context.put("access_level", "member");
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM", project);
org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newMember, TurbineUtils.getUser(data), TurbineUtils.GetSystemName() + " Access Granted for " + project.getName());
}
@@ -160,7 +160,7 @@ public class ManageProjectAccess extends SecureAction {
context.put("process", "Transfer to the archive.");
context.put("system", TurbineUtils.GetSystemName());
context.put("access_level", "collaborator");
- context.put("admin_email", AdminUtils.getAdminEmailId());
+ context.put("admin_email", XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM", project);
org.nrg.xnat.turbine.modules.actions.ProcessAccessRequest.SendAccessApprovalEmail(context, newMember, TurbineUtils.getUser(data), TurbineUtils.GetSystemName() + " Access Granted for " + project.getName());
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/MatchPrearchiveSessions.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/MatchPrearchiveSessions.java
index ecccb7c4dc72791787eed62dfa966a2e1e2a6a02..13bcaaf64e76cc16d08e2e428349956ad3688a29 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/MatchPrearchiveSessions.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/MatchPrearchiveSessions.java
@@ -10,15 +10,13 @@
*/
package org.nrg.xnat.turbine.modules.actions;
-import java.io.File;
-
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.base.BaseElement;
import org.nrg.xdat.om.XnatImagescandata;
import org.nrg.xdat.om.XnatImagesessiondata;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFTItem;
import org.nrg.xft.schema.Wrappers.XMLWrapper.SAXReader;
@@ -26,6 +24,8 @@ import org.nrg.xft.security.UserI;
import org.nrg.xnat.archive.BatchTransfer;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
+import java.io.File;
+
public class MatchPrearchiveSessions extends SecureAction {
/* (non-Javadoc)
@@ -33,14 +33,14 @@ public class MatchPrearchiveSessions extends SecureAction {
*/
@Override
public void doPerform(RunData data, Context context) throws Exception {
- Integer num= ((Integer)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedInteger("num_sessions",data));
- BatchTransfer bt = new BatchTransfer(TurbineUtils.GetFullServerPath(),TurbineUtils.GetSystemName(),AdminUtils.getAdminEmailId());
+ Integer num= TurbineUtils.GetPassedInteger("num_sessions", data);
+ BatchTransfer bt = new BatchTransfer(TurbineUtils.GetFullServerPath(), TurbineUtils.GetSystemName(), XDAT.getSiteConfigPreferences().getAdminEmail());
UserI user =TurbineUtils.getUser(data);
- bt.setUser((UserI)user);
+ bt.setUser(user);
String project = (String)TurbineUtils.GetPassedParameter("project", data);
if (num !=null)
{
- for (int h=0;h<=num.intValue();h++)
+ for (int h = 0; h <= num; h++)
{
String sessionFolder = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("session" + h,data));
String match = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("match" + h,data));
@@ -82,7 +82,7 @@ public class MatchPrearchiveSessions extends SecureAction {
SAXReader reader = new SAXReader(TurbineUtils.getUser(data));
XFTItem item = reader.parse(xml.getAbsolutePath());
- XnatImagesessiondata mr = (XnatImagesessiondata)XnatImagesessiondata.getXnatImagesessiondatasById(match, user, false);
+ XnatImagesessiondata mr = XnatImagesessiondata.getXnatImagesessiondatasById(match, user, false);
int k = 0;
while(TurbineUtils.HasPassedParameter("match" + h + ".scan" + k + "_id", data)){
@@ -90,10 +90,10 @@ public class MatchPrearchiveSessions extends SecureAction {
String use = (String)TurbineUtils.GetPassedParameter("match" + h + ".scan" + k + "_use", data);
String t = (String)TurbineUtils.GetPassedParameter("match" + h + ".scan" + k + "_type", data);
- XnatImagescandata scan = (XnatImagescandata) mr.getScanById(id);
+ XnatImagescandata scan = mr.getScanById(id);
if (scan==null){
XnatImagesessiondata tempMR= (XnatImagesessiondata)BaseElement.GetGeneratedItem(item);
- scan =(XnatImagescandata)tempMR.getScanById(id);
+ scan = tempMR.getScanById(id);
if (scan!=null){
mr.setScans_scan(scan);
}
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 942200b051ffcaa4582040e6315272e310e0881f..dc2d33e1201b41f9efc719c0646bf816b1f8a22f 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
@@ -25,6 +25,7 @@ import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
import org.nrg.pipeline.PipelineManager;
import org.nrg.pipeline.XnatPipelineLauncher;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.model.ArcPipelineparameterdataI;
import org.nrg.xdat.om.WrkWorkflowdata;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
@@ -108,7 +109,7 @@ public class PipelineActions extends SecureAction{
private XnatPipelineLauncher getGenericCommonParameters(RunData data, Context context, String projectId, String step, ItemI item) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data,context);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
UserI user = TurbineUtils.getUser(data);
xnatPipelineLauncher.setNeedsBuildDir(true);
@@ -185,7 +186,7 @@ public class PipelineActions extends SecureAction{
}
} catch (Exception e){
logger.error("",e);
- data.setMessage("<p><img src=\"/fcon/images/error.gif\">The build process failed to launch. Please contact the <a href=\"mailto:" + AdminUtils.getAdminEmailId() + "?subject=Failed to launch build \">NRG techdesk</a>");
+ data.setMessage("<p><img src=\"/fcon/images/error.gif\">The build process failed to launch. Please contact the <a href=\"mailto:" + XDAT.getSiteConfigPreferences().getAdminEmail() + "?subject=Failed to launch build \">NRG techdesk</a>");
data.setScreenTemplate("Error.vm");
}
}
@@ -193,7 +194,7 @@ public class PipelineActions extends SecureAction{
private XnatPipelineLauncher getCommonParameters(RunData data, Context context, String projectId, String pipelineName, String step) throws Exception {
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data,context);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
xnatPipelineLauncher.setPipelineName(pipelineName);
UserI user = TurbineUtils.getUser(data);
@@ -203,9 +204,9 @@ public class PipelineActions extends SecureAction{
xnatPipelineLauncher.setDataType("xnat:mrSessionData");
xnatPipelineLauncher.setParameter("useremail", user.getEmail());
xnatPipelineLauncher.setParameter("userfullname", XnatPipelineLauncher.getUserName(user));
- xnatPipelineLauncher.setParameter("adminemail", AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setParameter("adminemail", XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setParameter("xnatserver", TurbineUtils.GetSystemName());
- xnatPipelineLauncher.setParameter("mailhost", AdminUtils.getMailServer());
+ xnatPipelineLauncher.setParameter("mailhost", XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
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/ProcessAccessRequest.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ProcessAccessRequest.java
index c927eca91e4d87ff8b55854667e50abe9cb3cd1c..73d77bda5d7ff9af0b43c80246ef770a9911a9d1 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ProcessAccessRequest.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ProcessAccessRequest.java
@@ -89,18 +89,18 @@ public class ProcessAccessRequest extends SecureAction {
context.put("user",user);
context.put("server",TurbineUtils.GetFullServerPath());
context.put("system",TurbineUtils.GetSystemName());
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",project);
StringWriter sw = new StringWriter();
Template template =Velocity.getTemplate("/screens/RequestProjectAccessDenialEmail.vm");
template.merge(context,sw);
String message= sw.toString();
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
String subject = TurbineUtils.GetSystemName() + " Access Request for " + project.getName() + " Denied";
try {
- XDAT.getMailService().sendHtmlMessage(from, other.getEmail(), user.getEmail(), AdminUtils.getAdminEmailId(), subject, message);
+ XDAT.getMailService().sendHtmlMessage(from, other.getEmail(), user.getEmail(), XDAT.getSiteConfigPreferences().getAdminEmail(), subject, message);
} catch (Exception e) {
logger.error("Unable to send mail",e);
throw e;
@@ -174,11 +174,11 @@ public class ProcessAccessRequest extends SecureAction {
context.put("process","Transfer to the archive.");
context.put("system",TurbineUtils.GetSystemName());
context.put("access_level",access_level);
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",project);
final ArrayList<String> ownerEmails = project.getOwnerEmails();
String[] projectOwnerEmails = ownerEmails.toArray(new String[ownerEmails.size()]);
- SendAccessApprovalEmail(context,AdminUtils.getAdminEmailId(),new String[]{other.getEmail()},projectOwnerEmails,new String[]{AdminUtils.getAdminEmailId()},TurbineUtils.GetSystemName() + " Access Request for " + project.getName() + " Approved");
+ SendAccessApprovalEmail(context,XDAT.getSiteConfigPreferences().getAdminEmail(),new String[]{other.getEmail()},projectOwnerEmails,new String[]{XDAT.getSiteConfigPreferences().getAdminEmail()},TurbineUtils.GetSystemName() + " Access Request for " + project.getName() + " Approved");
}
//data.setScreenTemplate("XDATScreen_manage_xnat_projectData.vm");
//data.setScreenTemplate("/xnat_projectData/xnat_projectData_summary_management.vm");
@@ -188,7 +188,7 @@ public class ProcessAccessRequest extends SecureAction {
}
public static void SendAccessApprovalEmail(Context context, String otherEmail, UserI user, String subject) throws Exception {
- String admin = AdminUtils.getAdminEmailId();
+ String admin = XDAT.getSiteConfigPreferences().getAdminEmail();
SendAccessApprovalEmail(context, admin, new String[]{otherEmail}, new String[]{user.getEmail()}, new String[]{admin}, subject);
}
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 a42b5801ba0f62963de1ec1aa53f4c5c831564e8..8d7262a6b1e097de386f91dded72f2086ac5ebbd 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
@@ -32,6 +32,7 @@ import org.nrg.pipeline.xmlbeans.ParameterData;
import org.nrg.pipeline.xmlbeans.ParameterData.Values;
import org.nrg.pipeline.xmlbeans.ParametersDocument;
import org.nrg.pipeline.xmlbeans.ParametersDocument.Parameters;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.search.DisplaySearch;
import org.nrg.xdat.turbine.modules.actions.ListingAction;
import org.nrg.xdat.turbine.utils.AdminUtils;
@@ -106,7 +107,7 @@ public class QDECAction extends ListingAction{
//Launch the job
String pipelineName = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("hdn_pipelinename",data));
XnatPipelineLauncher xnatPipelineLauncher = new XnatPipelineLauncher(data,context);
- xnatPipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ xnatPipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
xnatPipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
xnatPipelineLauncher.setPipelineName(pipelineName);
xnatPipelineLauncher.setId(id);
@@ -122,13 +123,13 @@ public class QDECAction extends ListingAction{
data.setMessage( "<p><b>Your QDEC analysis was successfully launched. Status email will be sent to you upon its completion.</b></p>");
data.setScreenTemplate("ClosePage.vm");
}catch(Exception e) {
- data.setMessage("<p><b>The QDEC Analysis process could not be launched. Please contact <A HREF=\"mailto:"+AdminUtils.getAdminEmailId()+"?subject=Error: Performing QDEC Group Analysis" + "\">Report Error to" +TurbineUtils.GetSystemName() + " Techdesk</A></b></p>");
+ data.setMessage("<p><b>The QDEC Analysis process could not be launched. Please contact <A HREF=\"mailto:"+XDAT.getSiteConfigPreferences().getAdminEmail()+"?subject=Error: Performing QDEC Group Analysis" + "\">Report Error to" +TurbineUtils.GetSystemName() + " Techdesk</A></b></p>");
data.setScreenTemplate("Error.vm");
}
}
private ArrayList<String> removeSpaces(ArrayList<String> inList) {
- ArrayList<String> rtn = new ArrayList<String>();
+ ArrayList<String> rtn = new ArrayList<>();
for (String aStr: inList) {
rtn.add(StringUtils.deleteWhitespace(aStr));
}
@@ -200,7 +201,7 @@ public class QDECAction extends ListingAction{
param = parameters.addNewParameter();
param.setName("adminemail");
- param.addNewValues().setUnique(AdminUtils.getAdminEmailId());
+ param.addNewValues().setUnique(XDAT.getSiteConfigPreferences().getAdminEmail());
param = parameters.addNewParameter();
param.setName("xnatserver");
@@ -209,7 +210,7 @@ public class QDECAction extends ListingAction{
param = parameters.addNewParameter();
param.setName("mailhost");
- param.addNewValues().setUnique( AdminUtils.getMailServer());
+ param.addNewValues().setUnique( XDAT.getSiteConfigPreferences().getSmtpServer().get("host"));
return parameters;
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/ReportIssue.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/ReportIssue.java
index 1a0582049fab4e51623f7296bb63b20096ed5dad..17dd0e7262d0f4275bf1d9b211e3018b00c7aa88 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/ReportIssue.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/ReportIssue.java
@@ -48,7 +48,7 @@ public class ReportIssue extends SecureAction {
@Override
public void doPerform(RunData data, Context context) throws Exception {
- final String adminEmail = XFT.GetAdminEmail();
+ final String adminEmail = XDAT.getSiteConfigPreferences().getAdminEmail();
final UserI user = TurbineUtils.getUser(data);
final ParameterParser parameters = data.getParameters();
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/RequestAccess.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/RequestAccess.java
index 8d6165a450ca2f2978ab042cf50ec54883960956..a769213b7db1808663707e604ff8c035f50c5e81 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/RequestAccess.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/RequestAccess.java
@@ -49,7 +49,7 @@ public class RequestAccess extends SecureAction {
context.put("server",TurbineUtils.GetFullServerPath());
context.put("process","Transfer to the archive.");
context.put("system",TurbineUtils.GetSystemName());
- context.put("admin_email",AdminUtils.getAdminEmailId());
+ context.put("admin_email",XDAT.getSiteConfigPreferences().getAdminEmail());
context.put("projectOM",project);
context.put("access_level",access_level);
context.put("comments",comments);
@@ -81,10 +81,10 @@ public class RequestAccess extends SecureAction {
String[] bcc = null;
if(ArcSpecManager.GetInstance().getEmailspecifications_projectAccess()){
- bcc = new String[] { AdminUtils.getAdminEmailId() };
+ bcc = new String[] { XDAT.getSiteConfigPreferences().getAdminEmail() };
}
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
String subject = TurbineUtils.GetSystemName() + " Access Request for " + project.getName();
try {
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/SampleBuild.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/SampleBuild.java
index aae9fcdb7f1700e563185df7f74dd5130b314ade..79eef6cde872160d3026d5483c5a8aff9a1e65e8 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/SampleBuild.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/SampleBuild.java
@@ -15,9 +15,9 @@ import org.apache.log4j.Logger;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
import org.nrg.pipeline.XnatPipelineLauncher;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatMrsessiondata;
import org.nrg.xdat.turbine.modules.actions.SecureAction;
-import org.nrg.xdat.turbine.utils.AdminUtils;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.ItemI;
import org.nrg.xnat.turbine.utils.ArcSpecManager;
@@ -37,17 +37,18 @@ public class SampleBuild extends SecureAction
}
String xnat = ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("xnat",data));
XnatPipelineLauncher pipelineLauncher = new XnatPipelineLauncher(data,context);
- pipelineLauncher.setAdmin_email(AdminUtils.getAdminEmailId());
+ pipelineLauncher.setAdmin_email(XDAT.getSiteConfigPreferences().getAdminEmail());
pipelineLauncher.setAlwaysEmailAdmin(ArcSpecManager.GetInstance().getEmailspecifications_pipeline());
pipelineLauncher.setId(mr.getId());
pipelineLauncher.setDataType("xnat:mrSessionData");
pipelineLauncher.setPipelineName(pipelineName);
pipelineLauncher.setParameter("sessionId",mr.getId());
pipelineLauncher.setParameter("xnat",xnat);
- String emailsStr = TurbineUtils.getUser(data).getEmail() + "," + ((String)org.nrg.xdat.turbine.utils.TurbineUtils.GetPassedParameter("emailField",data));
+ String emailsStr = XDAT.getUserDetails().getEmail() + "," + TurbineUtils.GetPassedParameter("emailField", data);
String[] emails = emailsStr.trim().split(",");
- for (int i = 0 ; i < emails.length; i++)
- pipelineLauncher.notify(emails[i]);
+ for (final String email : emails) {
+ pipelineLauncher.notify(email);
+ }
boolean success = pipelineLauncher.launch();
if (success) {
data.setMessage("Build was launched successfully");
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/actions/XDATRegisterUser.java b/src/main/java/org/nrg/xnat/turbine/modules/actions/XDATRegisterUser.java
index ce98b18771f2b2458f751ebf0a9a161090d0bddf..b61c959281a8ef13a7567c88ec9bf8d04ab9862a 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/actions/XDATRegisterUser.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/actions/XDATRegisterUser.java
@@ -94,13 +94,13 @@ public class XDATRegisterUser extends org.nrg.xdat.turbine.modules.actions.XDATR
context.put("user", user);
action.doPerform(data, context);
} else if (!StringUtils.isEmpty(nextAction) && !nextAction.contains("XDATLoginUser") && !nextAction.equals(Turbine.getConfiguration().getString("action.login"))) {
- if (XFT.GetUserRegistration() & !XDAT.verificationOn()) {
+ if (XDAT.getSiteConfigPreferences().getUserRegistration() & !XDAT.verificationOn()) {
data.setAction(nextAction);
VelocityAction action = (VelocityAction) ActionLoader.getInstance().getInstance(nextAction);
action.doPerform(data, context);
}
} else if (!StringUtils.isEmpty(nextPage) && !nextPage.equals(Turbine.getConfiguration().getString("template.home"))) {
- if (XFT.GetUserRegistration() && !XDAT.verificationOn()) {
+ if (XDAT.getSiteConfigPreferences().getUserRegistration() && !XDAT.verificationOn()) {
data.setScreenTemplate(nextPage);
}
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/BuildPipelineParameters.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/BuildPipelineParameters.java
index a93e8e809d5a151575ba5b5e6da21b47aedf9970..709dd0bb80be4d4597947e4952251f33d857ca4b 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/BuildPipelineParameters.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/BuildPipelineParameters.java
@@ -13,14 +13,13 @@ package org.nrg.xnat.turbine.modules.screens;
import org.apache.turbine.util.RunData;
import org.apache.velocity.context.Context;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.XnatMrsessiondata;
import org.nrg.xdat.turbine.modules.screens.SecureReport;
import org.nrg.xdat.turbine.utils.TurbineUtils;
import org.nrg.xft.XFT;
-public class BuildPipelineParameters extends SecureReport
-{
-
+public class BuildPipelineParameters extends SecureReport {
public void preProcessing(RunData data, Context context)
{
TurbineUtils.InstanciatePassedItemForScreenUse(data,context);
@@ -55,7 +54,7 @@ public class BuildPipelineParameters extends SecureReport
return;
}catch(Exception e) {
String errorString = "<img src=\"/cnda1/images/error.gif\"> Error in the Build Spec file document for the pipeline " + context.get("pipelineName") ;
- errorString += "<p>Please contact the <a href=\"mailto:"+XFT.GetAdminEmail()+"?subject=Error in Build Spec file for " + mr.getSessionType() + " pipeline " + pipelineName + "\">CNL techdesk</a> to resolve the error.</p>";
+ errorString += "<p>Please contact the <a href=\"mailto:"+XDAT.getSiteConfigPreferences().getAdminEmail()+"?subject=Error in Build Spec file for " + mr.getSessionType() + " pipeline " + pipelineName + "\">CNL techdesk</a> to resolve the error.</p>";
data.setMessage(errorString);
data.getParameters().add("exception",e.getMessage());
data.setScreenTemplate("Error.vm");
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/DefaultPipelineScreen.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/DefaultPipelineScreen.java
index db9a989c8034e9e9306182acdf8541a25e9cac6d..91d8afebd4ca08e77feb7fae0aaea0ae8426f815 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/DefaultPipelineScreen.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/DefaultPipelineScreen.java
@@ -303,15 +303,7 @@ public abstract class DefaultPipelineScreen extends SecureReport {
Configuration config = XDAT.getConfigService().getConfig(toolName, fileName, Scope.Project, project);
if (config != null && config.getContents() != null) {
- String scanTypeCsv = config.getContents().trim();
- List<String> scanTypeList = Lists.transform(Lists.newArrayList(scanTypeCsv.split(",")), new Function<String, String>() {
- @Override
- public String apply(String input) {
- return input.trim();
- }
- });
-
- return ((XnatImagesessiondata) om).getScansByTypeList(scanTypeList);
+ return ((XnatImagesessiondata) om).getScansByTypeCsv(config.getContents().trim());
} else {
return Lists.newArrayList();
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen.java
index adf02c39a2cbc606a9d91a7df714f84828a56dfb..73ecbe0b7c4df1f27f4ce8a09b835b715f62835f 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen.java
@@ -16,6 +16,7 @@ import org.apache.turbine.util.RunData;
import org.apache.velocity.app.FieldMethodizer;
import org.apache.velocity.context.Context;
import org.nrg.pipeline.PipelineManager;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.base.BaseElement;
import org.nrg.xdat.model.ArcProjectPipelineI;
import org.nrg.xdat.model.WrkAbstractexecutionenvironmentI;
@@ -252,7 +253,7 @@ public abstract class PipelineScreen extends SecureReport {
}
}
if (rtn == null) {
- message = "Pipeline with step id " + pipeline_step + " is not defined. Please contact your site administrator <a href=\"mailto:" +XFT.GetAdminEmail() +"?subject=Invalid Pipeline Step " + pipeline_step + " for " + item.getXSIType() + "\">Report problem</A>";
+ message = "Pipeline with step id " + pipeline_step + " is not defined. Please contact your site administrator <a href=\"mailto:" + XDAT.getSiteConfigPreferences().getAdminEmail() + "?subject=Invalid Pipeline Step " + pipeline_step + " for " + item.getXSIType() + "\">Report problem</A>";
}
return rtn;
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen_set_site_parameters.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen_set_site_parameters.java
index 3745e506f4811fb26f04e84e2bd31e8b1c2a6dbe..d53b11b3be94338bf511d9c202e74377c72fb6ca 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen_set_site_parameters.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/PipelineScreen_set_site_parameters.java
@@ -19,12 +19,12 @@ import org.nrg.pipeline.xmlbeans.PipelineData.Documentation.InputParameters;
import org.nrg.pipeline.xmlbeans.PipelineData.Documentation.InputParameters.Parameter;
import org.nrg.pipeline.xmlbeans.PipelineData.Documentation.InputParameters.Parameter.Values;
import org.nrg.pipeline.xmlbeans.PipelineDocument;
+import org.nrg.xdat.XDAT;
import org.nrg.xdat.om.PipePipelinedetails;
import org.nrg.xdat.om.PipePipelinedetailsParameter;
import org.nrg.xdat.om.PipePipelinerepository;
import org.nrg.xdat.turbine.modules.screens.AdminEditScreenA;
import org.nrg.xdat.turbine.utils.TurbineUtils;
-import org.nrg.xft.XFT;
import org.nrg.xft.event.EventUtils;
import org.nrg.xft.security.UserI;
import org.nrg.xft.utils.SaveItemHelper;
@@ -81,14 +81,14 @@ public class PipelineScreen_set_site_parameters extends AdminEditScreenA{
data.setMessage("The pipeline has been added to the repository");
data.setScreenTemplate("ClosePage.vm");
} catch (Exception e) {
- data.setMessage("The pipeline could not be added to the repository. Please contact " + XFT.GetAdminEmail() );
+ data.setMessage("The pipeline could not be added to the repository. Please contact " + XDAT.getSiteConfigPreferences().getAdminEmail() );
data.setScreenTemplate("Error.vm");
}
}
}catch(Exception e) {
logger.error(e);
e.printStackTrace();
- data.setMessage("The pipeline could not be added to the repository. Please contact " + XFT.GetAdminEmail() );
+ data.setMessage("The pipeline could not be added to the repository. Please contact " + XDAT.getSiteConfigPreferences().getAdminEmail());
data.setScreenTemplate("Error.vm");
}
}
diff --git a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_UpdateUser.java b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_UpdateUser.java
index c524493f5cb5c42517d7a85d86707f1601f11887..bbe5853cbcf632eb7aba1d6c8ccc8ffeb74eaf8e 100644
--- a/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_UpdateUser.java
+++ b/src/main/java/org/nrg/xnat/turbine/modules/screens/XDATScreen_UpdateUser.java
@@ -46,22 +46,14 @@ public class XDATScreen_UpdateUser extends SecureScreen {
}
c.put("user", XDAT.getUserDetails());
- if (TurbineUtils.GetPassedParameter("popup", data) != null) {
- if (((String) TurbineUtils.GetPassedParameter("popup", data)).equalsIgnoreCase("true")) {
- c.put("popup", "true");
- } else {
- c.put("popup", "false");
- }
- } else {
- c.put("popup", "false");
- }
+ checkForPopup(data, c);
c.put("displayManager", DisplayManager.GetInstance());
c.put("systemName", TurbineUtils.GetSystemName());
c.put("esc", new EscapeTool());
- c.put("showReason", XFT.getShowChangeJustification());
- c.put("requireReason", XFT.getRequireChangeJustification());
+ c.put("showReason", XDAT.getSiteConfigPreferences().getShowChangeJustification());
+ c.put("requireReason", XDAT.getSiteConfigPreferences().getRequireChangeJustification());
try{
c.put("siteConfig", XDAT.getSiteConfiguration());
}catch(ConfigServiceException ignored){
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 53820e7e6e35ef2302d3a05678fcbf98e496faca..c39e128942e2ea2c4644712e08926c1c9ea141b7 100644
--- a/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java
+++ b/src/main/java/org/nrg/xnat/turbine/utils/ArcSpecManager.java
@@ -61,131 +61,129 @@ public class ArcSpecManager {
logger.info("Initializing ArcSpec...");
arcSpec = GetFreshInstance();
- if (arcSpec!=null){
-
- if (arcSpec.getSiteAdminEmail()!=null && !arcSpec.getSiteAdminEmail().equals("")){
- XFT.SetAdminEmail(arcSpec.getSiteAdminEmail());
- }else{
- arcSpec.setSiteAdminEmail(XFT.GetAdminEmail());
- }
-
- if (arcSpec.getSiteUrl()!=null && !arcSpec.getSiteUrl().equals("")){
- XFT.SetSiteURL(arcSpec.getSiteUrl());
- }else{
- arcSpec.setSiteUrl(XFT.GetSiteURL());
- }
-
- if (arcSpec.getSiteId()!=null && !arcSpec.getSiteId().equals("")){
- XFT.SetSiteID(arcSpec.getSiteId());
- }else{
- arcSpec.setSiteId("");
- }
-
- if (arcSpec.getSmtpHost()!=null && !arcSpec.getSmtpHost().equals("")){
- XFT.SetAdminEmailHost(arcSpec.getSmtpHost());
- }else{
- arcSpec.setSmtpHost(XFT.GetAdminEmailHost());
- }
-
- if (arcSpec.getEnableNewRegistrations()!=null){
- XFT.SetUserRegistration(arcSpec.getEnableNewRegistrations().toString());
- }else{
- arcSpec.setEnableNewRegistrations(XFT.GetUserRegistration());
- }
-
- if (arcSpec.getRequireLogin()!=null){
- XFT.SetRequireLogin(arcSpec.getRequireLogin().toString());
- }else{
- arcSpec.setRequireLogin(XFT.GetRequireLogin());
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getPipelinepath()!=null){
- XFT.SetPipelinePath(arcSpec.getGlobalpaths().getPipelinepath());
- }else{
- if (arcSpec.getGlobalpaths()!=null){
- arcSpec.getGlobalpaths().setPipelinepath(XFT.GetPipelinePath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getArchivepath()!=null){
- XFT.SetArchiveRootPath(arcSpec.getGlobalpaths().getArchivepath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.GetArchiveRootPath()!=null){
- arcSpec.getGlobalpaths().setArchivepath(XFT.GetArchiveRootPath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getCachepath()!=null){
- XFT.SetCachePath(arcSpec.getGlobalpaths().getCachepath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.GetCachePath()!=null){
- arcSpec.getGlobalpaths().setCachepath(XFT.GetCachePath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getFtppath()!=null){
- XFT.setFtpPath(arcSpec.getGlobalpaths().getFtppath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.getFtpPath()!=null){
- arcSpec.getGlobalpaths().setFtppath(XFT.getFtpPath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getBuildpath()!=null){
- XFT.setFtpPath(arcSpec.getGlobalpaths().getBuildpath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.getBuildPath()!=null){
- arcSpec.getGlobalpaths().setBuildpath(XFT.getBuildPath());
- }
- }
-
- if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getPrearchivepath()!=null){
- XFT.SetPrearchivePath(arcSpec.getGlobalpaths().getPrearchivepath());
- }else{
- if (arcSpec.getGlobalpaths()!=null && XFT.GetPrearchivePath()!=null){
- arcSpec.getGlobalpaths().setPrearchivepath(XFT.GetPrearchivePath());
- }
- }
-
-
- //set email defaults
- if (arcSpec.getEmailspecifications_newUserRegistration()==null){
- arcSpec.setEmailspecifications_newUserRegistration(true);
- }
- if (arcSpec.getEmailspecifications_pageEmail()==null){
- arcSpec.setEmailspecifications_pageEmail(true);
- }
- if (arcSpec.getEmailspecifications_pipeline()==null){
- arcSpec.setEmailspecifications_pipeline(true);
- }
- if (arcSpec.getEmailspecifications_projectAccess()==null){
- arcSpec.setEmailspecifications_projectAccess(true);
- }
- if (arcSpec.getEmailspecifications_transfer()==null){
- arcSpec.setEmailspecifications_transfer(true);
- }
- //end email defaults
-
- if (arcSpec.getEmailspecifications_newUserRegistration()!=null){
- AdminUtils.SetNewUserRegistrationsEmail(arcSpec.getEmailspecifications_newUserRegistration());
- }
-
- if (arcSpec.getEmailspecifications_pageEmail()!=null){
- AdminUtils.SetPageEmail(arcSpec.getEmailspecifications_pageEmail());
- }
-
- if (arcSpec.getDcm_appletLink()==null){
- arcSpec.setDcm_appletLink(Boolean.TRUE);
- }
-
- if (arcSpec.getEnableCsrfToken()!=null){
- XFT.SetEnableCsrfToken(arcSpec.getEnableCsrfToken().toString());
- }else{
- arcSpec.setEnableCsrfToken(XFT.GetEnableCsrfToken());
- }
-
-
- }
+// if (arcSpec!=null){
+//
+// if (arcSpec.getSiteAdminEmail()!=null && !arcSpec.getSiteAdminEmail().equals("")){
+// XFT.SetAdminEmail(arcSpec.getSiteAdminEmail());
+// }else{
+// arcSpec.setSiteAdminEmail(XDAT.getSiteConfigPreferences().getAdminEmail());
+// }
+//
+// if (arcSpec.getSiteUrl()!=null && !arcSpec.getSiteUrl().equals("")){
+// XFT.SetSiteURL(arcSpec.getSiteUrl());
+// }else{
+// arcSpec.setSiteUrl(XDAT.getSiteConfigPreferences().getSiteUrl());
+// }
+//
+// if (arcSpec.getSiteId()!=null && !arcSpec.getSiteId().equals("")){
+// XFT.SetSiteID(arcSpec.getSiteId());
+// }else{
+// arcSpec.setSiteId("");
+// }
+//
+// if (arcSpec.getSmtpHost()!=null && !arcSpec.getSmtpHost().equals("")){
+// XFT.SetAdminEmailHost(arcSpec.getSmtpHost());
+// }else{
+// arcSpec.setSmtpHost(XFT.GetAdminEmailHost());
+// }
+//
+// if (arcSpec.getEnableNewRegistrations()!=null){
+// XFT.SetUserRegistration(arcSpec.getEnableNewRegistrations().toString());
+// }else{
+// arcSpec.setEnableNewRegistrations(XDAT.getSiteConfigPreferences().getUserRegistration());
+// }
+//
+// if (arcSpec.getRequireLogin()!=null){
+// XFT.SetRequireLogin(arcSpec.getRequireLogin().toString());
+// }else{
+// arcSpec.setRequireLogin(XDAT.getSiteConfigPreferences().getRequireLogin());
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getPipelinepath()!=null){
+// XFT.SetPipelinePath(arcSpec.getGlobalpaths().getPipelinepath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null){
+// arcSpec.getGlobalpaths().setPipelinepath(XDAT.getSiteConfigPreferences().getAdminEmail());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getArchivepath()!=null){
+// XFT.SetArchiveRootPath(arcSpec.getGlobalpaths().getArchivepath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XFT.GetArchiveRootPath()!=null){
+// arcSpec.getGlobalpaths().setArchivepath(XFT.GetArchiveRootPath());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getCachepath()!=null){
+// XFT.SetCachePath(arcSpec.getGlobalpaths().getCachepath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XDAT.getSiteConfigPreferences().getCachePath()!=null){
+// arcSpec.getGlobalpaths().setCachepath(XDAT.getSiteConfigPreferences().getCachePath());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getFtppath()!=null){
+// XFT.setFtpPath(arcSpec.getGlobalpaths().getFtppath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XFT.getFtpPath()!=null){
+// arcSpec.getGlobalpaths().setFtppath(XFT.getFtpPath());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getBuildpath()!=null){
+// XFT.setFtpPath(arcSpec.getGlobalpaths().getBuildpath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XFT.getBuildPath()!=null){
+// arcSpec.getGlobalpaths().setBuildpath(XFT.getBuildPath());
+// }
+// }
+//
+// if (arcSpec.getGlobalpaths()!=null && arcSpec.getGlobalpaths().getPrearchivepath()!=null){
+// XFT.SetPrearchivePath(arcSpec.getGlobalpaths().getPrearchivepath());
+// }else{
+// if (arcSpec.getGlobalpaths()!=null && XFT.GetPrearchivePath()!=null){
+// arcSpec.getGlobalpaths().setPrearchivepath(XFT.GetPrearchivePath());
+// }
+// }
+//
+//
+// //set email defaults
+// if (arcSpec.getEmailspecifications_newUserRegistration()==null){
+// arcSpec.setEmailspecifications_newUserRegistration(true);
+// }
+// if (arcSpec.getEmailspecifications_pageEmail()==null){
+// arcSpec.setEmailspecifications_pageEmail(true);
+// }
+// if (arcSpec.getEmailspecifications_pipeline()==null){
+// arcSpec.setEmailspecifications_pipeline(true);
+// }
+// if (arcSpec.getEmailspecifications_projectAccess()==null){
+// arcSpec.setEmailspecifications_projectAccess(true);
+// }
+// if (arcSpec.getEmailspecifications_transfer()==null){
+// arcSpec.setEmailspecifications_transfer(true);
+// }
+// //end email defaults
+//
+// if (arcSpec.getEmailspecifications_newUserRegistration()!=null){
+// AdminUtils.SetNewUserRegistrationsEmail(arcSpec.getEmailspecifications_newUserRegistration());
+// }
+//
+// if (arcSpec.getEmailspecifications_pageEmail()!=null){
+// AdminUtils.SetPageEmail(arcSpec.getEmailspecifications_pageEmail());
+// }
+//
+// if (arcSpec.getDcm_appletLink()==null){
+// arcSpec.setDcm_appletLink(Boolean.TRUE);
+// }
+//
+// if (arcSpec.getEnableCsrfToken()!=null){
+// XFT.SetEnableCsrfToken(arcSpec.getEnableCsrfToken().toString());
+// }else{
+// arcSpec.setEnableCsrfToken(XDAT.getSiteConfigPreferences().getEnableCsrfToken());
+// }
+// }
try {
if (arcSpec!=null){
@@ -228,45 +226,45 @@ public class ArcSpecManager {
public synchronized static ArcArchivespecification initialize(UserI user) throws XFTInitException, ElementNotFoundException, FieldNotFoundException, InvalidValueException {
arcSpec = new ArcArchivespecification(user);
- if (XFT.GetAdminEmail()!=null && !XFT.GetAdminEmail().equals("")) {
- arcSpec.setSiteAdminEmail(XFT.GetAdminEmail());
+ if (XDAT.getSiteConfigPreferences().getAdminEmail()!=null && !XDAT.getSiteConfigPreferences().getAdminEmail().equals("")) {
+ arcSpec.setSiteAdminEmail(XDAT.getSiteConfigPreferences().getAdminEmail());
}
- if (XFT.GetSiteURL()!=null && !XFT.GetSiteURL().equals("")) {
- arcSpec.setSiteUrl(XFT.GetSiteURL());
+ if (XDAT.getSiteConfigPreferences().getSiteUrl()!=null && !XDAT.getSiteConfigPreferences().getSiteUrl().equals("")) {
+ arcSpec.setSiteUrl(XDAT.getSiteConfigPreferences().getSiteUrl());
}
- if (XFT.GetAdminEmailHost()!=null && !XFT.GetAdminEmailHost().equals("")) {
- arcSpec.setSmtpHost(XFT.GetAdminEmailHost());
- }
-
- arcSpec.setEnableNewRegistrations(XFT.GetUserRegistration());
-
- arcSpec.setRequireLogin(XFT.GetRequireLogin());
- if (XFT.GetPipelinePath()!=null && !XFT.GetPipelinePath().equals("")) {
- arcSpec.setProperty("globalPaths/pipelinePath", XFT.GetPipelinePath());
- }
-
- if (XFT.GetArchiveRootPath()!=null && !XFT.GetArchiveRootPath().equals("")) {
- arcSpec.setProperty("globalPaths/archivePath", XFT.GetArchiveRootPath());
- }
-
- if (XFT.GetPrearchivePath()!=null && !XFT.GetPrearchivePath().equals("")) {
- arcSpec.setProperty("globalPaths/prearchivePath", XFT.GetPrearchivePath());
- }
-
- if (XFT.GetCachePath()!=null && !XFT.GetCachePath().equals("")) {
- arcSpec.setProperty("globalPaths/cachePath", XFT.GetCachePath());
- }
-
- if (XFT.getFtpPath()!=null && !XFT.getFtpPath().equals("")) {
- arcSpec.setProperty("globalPaths/ftpPath", XFT.getFtpPath());
- }
-
- if (XFT.getBuildPath()!=null && !XFT.getBuildPath().equals("")) {
- arcSpec.setProperty("globalPaths/buildPath", XFT.getBuildPath());
- }
- arcSpec.setEnableCsrfToken(XFT.GetEnableCsrfToken());
+// if (XFT.GetAdminEmailHost()!=null && !XFT.GetAdminEmailHost().equals("")) {
+// arcSpec.setSmtpHost(XFT.GetAdminEmailHost());
+// }
+//
+// arcSpec.setEnableNewRegistrations(XDAT.getSiteConfigPreferences().getUserRegistration());
+//
+// arcSpec.setRequireLogin(XDAT.getSiteConfigPreferences().getRequireLogin());
+// if (XDAT.getSiteConfigPreferences().getAdminEmail()!=null && !XDAT.getSiteConfigPreferences().getAdminEmail().equals("")) {
+// arcSpec.setProperty("globalPaths/pipelinePath", XDAT.getSiteConfigPreferences().getAdminEmail());
+// }
+//
+// if (XFT.GetArchiveRootPath()!=null && !XFT.GetArchiveRootPath().equals("")) {
+// arcSpec.setProperty("globalPaths/archivePath", XFT.GetArchiveRootPath());
+// }
+//
+// if (XFT.GetPrearchivePath()!=null && !XFT.GetPrearchivePath().equals("")) {
+// arcSpec.setProperty("globalPaths/prearchivePath", XFT.GetPrearchivePath());
+// }
+//
+// if (XDAT.getSiteConfigPreferences().getCachePath()!=null && !XDAT.getSiteConfigPreferences().getCachePath().equals("")) {
+// arcSpec.setProperty("globalPaths/cachePath", XDAT.getSiteConfigPreferences().getCachePath());
+// }
+//
+// if (XFT.getFtpPath()!=null && !XFT.getFtpPath().equals("")) {
+// arcSpec.setProperty("globalPaths/ftpPath", XFT.getFtpPath());
+// }
+//
+// if (XFT.getBuildPath()!=null && !XFT.getBuildPath().equals("")) {
+// arcSpec.setProperty("globalPaths/buildPath", XFT.getBuildPath());
+// }
+// arcSpec.setEnableCsrfToken(XFT.GetEnableCsrfToken());
return arcSpec;
}
diff --git a/src/main/java/org/nrg/xnat/turbine/utils/IDGenerator.java b/src/main/java/org/nrg/xnat/turbine/utils/IDGenerator.java
index a1a066810915a5d8867963a3b50a37bd5dd972fd..d71c1d7d92b67625ffa55fc8a7df7e8453de7d60 100644
--- a/src/main/java/org/nrg/xnat/turbine/utils/IDGenerator.java
+++ b/src/main/java/org/nrg/xnat/turbine/utils/IDGenerator.java
@@ -11,7 +11,7 @@
package org.nrg.xnat.turbine.utils;
import org.apache.commons.lang3.StringUtils;
-import org.nrg.xft.XFT;
+import org.nrg.xdat.XDAT;
import org.nrg.xft.XFTTable;
import org.nrg.xft.identifier.IDGeneratorI;
import org.nrg.xnat.services.impl.hibernate.HibernateHostInfoService;
@@ -53,7 +53,7 @@ public class IDGenerator implements IDGeneratorI {
}
/** The claimed i ds. */
- private static List<String> claimedIDs=new ArrayList<String>();
+ private static List<String> claimedIDs= new ArrayList<>();
/** The Constant lock. */
private static final Object lock=new Object();
@@ -80,7 +80,7 @@ public class IDGenerator implements IDGeneratorI {
site +="_V";
}
- String temp_id=null;
+ String temp_id;
XFTTable table = org.nrg.xft.search.TableSearch.Execute("SELECT DISTINCT " + column + " FROM (SELECT " + column + " FROM " + tableName + " WHERE " + column + " LIKE '" + site + "%' UNION SELECT DISTINCT " + column + " FROM " + tableName + "_history WHERE " + column + " LIKE '" + site + "%') SRCH;", null, null);
ArrayList al =table.convertColumnToArrayList(column.toLowerCase());
@@ -171,7 +171,7 @@ public class IDGenerator implements IDGeneratorI {
* @return the site id
*/
private String getSiteID(){
- String site_id = XFT.GetSiteID();
+ String site_id = XDAT.getSiteConfigPreferences().getSiteId();
site_id = StringUtils.replace(site_id, " ", "");
site_id = StringUtils.replace(site_id, "-", "_");
site_id = StringUtils.replace(site_id, "\"", "");
diff --git a/src/main/java/org/nrg/xnat/turbine/utils/ProjectAccessRequest.java b/src/main/java/org/nrg/xnat/turbine/utils/ProjectAccessRequest.java
index 08d261b0ba7af174a1471c8accd3096c46e4d4f9..660bb8c04853765661e93c76d8285af02dc5c1f0 100644
--- a/src/main/java/org/nrg/xnat/turbine/utils/ProjectAccessRequest.java
+++ b/src/main/java/org/nrg/xnat/turbine/utils/ProjectAccessRequest.java
@@ -486,10 +486,10 @@ public class ProjectAccessRequest {
String bcc = null;
if (ArcSpecManager.GetInstance().getEmailspecifications_projectAccess()) {
- bcc = AdminUtils.getAdminEmailId();
+ bcc = XDAT.getSiteConfigPreferences().getAdminEmail();
}
- String from = AdminUtils.getAdminEmailId();
+ String from = XDAT.getSiteConfigPreferences().getAdminEmail();
try {
XDAT.getMailService().sendHtmlMessage(from, invitee, user.getEmail(), bcc, subject, writer.toString());
diff --git a/src/main/java/org/nrg/xnat/utils/FileUtils.java b/src/main/java/org/nrg/xnat/utils/FileUtils.java
index 1234010afc69c4b7df6767774ca236a100b2dd6c..d7c11066ea1b93394de2d8af094fa54516f0b79f 100644
--- a/src/main/java/org/nrg/xnat/utils/FileUtils.java
+++ b/src/main/java/org/nrg/xnat/utils/FileUtils.java
@@ -13,6 +13,7 @@ package org.nrg.xnat.utils;
import org.apache.commons.lang3.StringUtils;
import org.apache.commons.logging.Log;
import org.apache.commons.logging.LogFactory;
+import org.nrg.xdat.XDAT;
import org.nrg.xft.XFT;
import java.io.BufferedReader;
@@ -27,7 +28,7 @@ public class FileUtils {
public static void moveToCache(final String project, final String subdir, final File src) throws IOException {
// should include a timestamp in folder name
if (src.exists()) {
- final File cache = (StringUtils.isBlank(subdir)) ? new File(XFT.GetCachePath(), project) : new File(new File(XFT.GetCachePath(), project), subdir);
+ final File cache = (StringUtils.isBlank(subdir)) ? new File(XDAT.getSiteConfigPreferences().getCachePath(), project) : new File(new File(XDAT.getSiteConfigPreferences().getCachePath(), project), subdir);
final File dest = new File(cache, org.nrg.xft.utils.FileUtils.renameWTimestamp(src.getName(), Calendar.getInstance().getTime()));
@@ -38,7 +39,7 @@ public class FileUtils {
public static File buildCachepath(String project, final String subdir, final String destName) {
if (project == null)
project = "Unknown";
- final File cache = (StringUtils.isEmpty(subdir)) ? new File(XFT.GetCachePath(), project) : new File(new File(XFT.GetCachePath(), project), subdir);
+ final File cache = (StringUtils.isEmpty(subdir)) ? new File(XDAT.getSiteConfigPreferences().getCachePath(), project) : new File(new File(XDAT.getSiteConfigPreferences().getCachePath(), project), subdir);
return new File(cache, org.nrg.xft.utils.FileUtils.renameWTimestamp(destName, Calendar.getInstance().getTime()));
}
@@ -144,7 +145,7 @@ public class FileUtils {
@SafeVarargs
public static <T extends String> File buildCacheSubDir(T... directories) {
- File last = new File(XFT.GetCachePath());
+ File last = new File(XDAT.getSiteConfigPreferences().getCachePath());
for (final String dir : directories) {
if (!StringUtils.isEmpty(dir)) {
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 a36dea2ddd51796e2f1cfcfca33354f2dd334e0e..84bcb3dc5c485cf07665a5e522e0b8152492207d 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
@@ -16,10 +16,10 @@ siteId:
label: Site ID
validation: required id onblur
description: "The id used to refer to this site (also used to generate database ids). The Site ID must start with a letter and contain only letters, numbers and underscores. It should be a short, one-word name or acronym which describes your site. No spaces or non-alphanumeric characters."
-siteDescriptionOption:
+siteDescriptionType:
kind: panel.display # make this a radio button group
- id: siteDescriptionOption
- name: siteDescriptionOption
+ id: siteDescriptionType
+ name: siteDescriptionType
label: Site Description
value: Select a site description option below
# onchange: # some javascript that toggles display of the elements below appropriately
@@ -31,10 +31,10 @@ siteDescriptionOptionPage:
kind: panel.input.checkbox # make this a radio button group
id: siteDescriptionOptionPage
label: "Page"
-siteDescriptionFile:
+siteDescriptionPage:
kind: panel.input.text
- id: siteDescriptionFile
- name: siteDescriptionFile
+ id: siteDescriptionPage
+ name: siteDescriptionPage
label: " "
description: "Specify a velocity template file to display on the login page"
siteDescriptionText:
@@ -43,6 +43,26 @@ siteDescriptionText:
name: siteDescriptionText
label: " "
description: "Specify a simple text description of this site"
+siteLoginLanding:
+ kind: panel.input.text
+ id: siteLoginLanding
+ name: siteLoginLanding
+ label: Site Login Landing
+siteLandingLayout:
+ kind: panel.input.text
+ id: siteLandingLayout
+ name: siteLandingLayout
+ label: Site Landing Layout
+siteHome:
+ kind: panel.input.text
+ id: siteHome
+ name: siteHome
+ label: Site Home
+siteHomeLayout:
+ kind: panel.input.text
+ id: siteHomeLayout
+ name: siteHomeLayout
+ label: Site Home Layout
siteUrl:
kind: panel.input.text
id: siteUrl
@@ -120,6 +140,11 @@ dataFolders:
label: Data Folders
validation: required id onblur
description: ""
+zipExtensions:
+ kind: panel.input.text
+ id: zipExtensions
+ name: zipExtensions
+ label: Zip Extensions
siteInfo:
kind: panel.form
@@ -133,11 +158,15 @@ siteInfo:
contents:
${siteId}
${siteUrl}
- ${siteDescriptionOption}
+ ${siteDescriptionType}
${siteDescriptionOptionText}
${siteDescriptionOptionPage}
- ${siteDescriptionFile}
+ ${siteDescriptionPage}
${siteDescriptionText}
+ ${siteLoginLanding}
+ ${siteLandingLayout}
+ ${siteHome}
+ ${siteHomeLayout}
adminInfo:
kind: panel.form
@@ -154,7 +183,7 @@ generalSecuritySettings:
securityChannel:
kind: panel.select.single
id: securityChannel
- name: security.channel
+ name: securityChannel
label: Security Channel
value: https
options:
@@ -167,7 +196,7 @@ generalSecuritySettings:
requireUserLogin:
kind: panel.input.checkbox
id: requireUserLogin
- name: require_login
+ name: requireLogin
label: Require User Login
description: "If checked, then only registered users will be able to access your site. If false, anyone visiting your site will automatically be logged in as 'guest' with access to public data."
@@ -184,7 +213,7 @@ userLoginsSessionControls:
sessionTimeout:
kind: panel.input.number
id: sessionTimeout
- name: security.token_timeout
+ name: aliasTokenTimeout
label: Session Timeout
value: 15
description: "Interval for timing out alias tokens. Uses PostgreSQL interval notation: http://www.postgresql.org/docs/9.0/static/functions-datetime.html"
@@ -226,17 +255,22 @@ userLoginsSessionControls:
failedLoginLockoutDuration:
kind: panel.input.number
id: failedLoginLockoutDuration
- name: security.max_failed_logins_lockout_duration
+ name: maxFailedLoginsLockoutDuration
label: Failed Login Lockout Duration
value: 0
description: Number of milliseconds to lock user accounts that have exceeded the max_failed_logins count. Select (3600000 for 1 hour, 86400000 for 24 hours)
userInactivityLockout:
kind: panel.input.number
id: userInactivityLockout
- name: security.inactivity_before_lockout
+ name: inactivityBeforeLockout
label: User Inactivity Lockout
value: 31556926
description: Number of seconds of inactivity before an account is disabled (31556926 for 1 year)
+ inactivityBeforeLockoutSchedule:
+ kind: panel.input.text
+ id: inactivityBeforeLockoutSchedule
+ name: inactivityBeforeLockoutSchedule
+ label: "User Inactivity Before Lockout Schedule"
passwords:
kind: panel.form
@@ -268,6 +302,19 @@ passwords:
label: Password History (Duration)
value: -1
description: "-1 to disable"
+ passwordExpirationType:
+ kind: panel.select.single
+ id: passwordExpirationType
+ name: passwordExpirationType
+ label: passwordExpirationType
+ value: Interval
+ options:
+ Interval:
+ label: Interval
+ value: Interval
+ Date:
+ label: Date
+ value: Date
passwordExpirationInterval:
kind: panel.input.number
id: passwordExpirationInterval
@@ -320,24 +367,49 @@ auditTrail:
enableAuditTrail:
kind: panel.input.checkbox
id: enableAuditTrail
- name: audit.enable
+ name: enableAuditTrail
label: Enable Audit Trail?
value: true
allowUserJustificationForChanges:
kind: panel.input.checkbox
id: allowUserJustificationForChanges
- name: audit.show_change_justification
+ name: allowUserJustificationForChanges
label: Allow User Justification For Changes
value: true
description: "Allow users to enter change justifications when modifying data"
requireUserJustificationForChanges:
kind: panel.input.checkbox
id: requireUserJustificationForChanges
- name: audit.require_change_justification
+ name: requireUserJustificationForChanges
label: Require User Justification For Changes
value: false
description: "Force users to enter change justifications when modifying data"
+securityServices:
+ kind: panel.form
+ name: securityServices
+ label: Security Services
+ contents:
+ securityServicesFeatureDefault:
+ kind: panel.input.text
+ id: securityServicesFeatureDefault
+ name: security.services.feature.default
+ label: Feature Default
+ securityServicesFeatureRepoDefault:
+ kind: panel.input.text
+ id: securityServicesFeatureRepoDefault
+ name: security.services.featureRepository.default
+ label: Feature Repository Default
+ securityServicesRoleDefault:
+ kind: panel.input.text
+ id: securityServicesRoleDefault
+ name: security.services.role.default
+ label: Role Default
+ securityServicesRoleRepositoryDefault:
+ kind: panel.input.text
+ id: securityServicesRoleRepositoryDefault
+ name: security.services.roleRepository.default
+ label: Role Repository Default
emailServerSettings:
kind: panel.form
@@ -352,6 +424,13 @@ emailServerSettings:
name: emailServerSettings
label: Mail Server Settings
contents:
+ smtpEnabled:
+ kind: panel.input.checkbox
+ id: smtpEnabled
+ name: smtp.enabled
+ label: "Enable SMTP?"
+ #value: true
+ checked: true
hostname:
kind: panel.input.text
name: host
@@ -409,6 +488,12 @@ emailServerSettings:
value: ''
element:
placeholder: localhost
+ emailPrefix:
+ kind: panel.input.text
+ name: emailPrefix
+ label: Email Prefix
+ element:
+ placeholder: XNAT
notifications:
kind: panel.form
@@ -441,62 +526,61 @@ notifications:
notifyAdminUserRegistration:
kind: panel.input.checkbox
id: notifyAdminUserRegistration
- name: "email:new_user_registration"
+ name: notifyAdminUserRegistration
label: "Notify Admin on User Registration"
value: true
description: "Whether to cc admin user on new user emails. Requires valid admin email address."
notifyAdminPipelineEmails:
kind: panel.input.checkbox
id: notifyAdminPipelineEmails
- name: "email:pipeline"
+ name: notifyAdminPipelineEmails
label: "Notify Admin on Pipeline Emails"
value: false
description: "Whether to cc admin user on pipeline processing submit. Requires valid admin email address."
notifyAdminProjectAccessRequest:
kind: panel.input.checkbox
id: notifyAdminProjectAccessRequest
- name: "email:project_access"
+ name: notifyAdminProjectAccessRequest
label: "Notify Admin on Project Access Request"
value: false
description: "Whether to cc admin user on user project access request. Requires valid admin email address."
notifyAdminSessionTransfer:
kind: panel.input.checkbox
id: notifyAdminSessionTransfer
- name: "email:transfer"
+ name: notifyAdminSessionTransfer
label: "Notify Admin on Session Transfer"
value: false
description: "Whether to cc admin user on session transfer by user. Requires valid admin email address."
emailRecipientErrorMessages:
kind: panel.input.email
id: emailRecipientErrorMessages
- name: "Notifications:Error"
+ name: emailRecipientErrorMessages
label: "Email Recipient: Error Messages"
description: "What email address should receive error emails"
emailRecipientIssueReports:
kind: panel.input.email
id: emailRecipientIssueReports
- name: "Notifications:Issues"
+ name: emailRecipientIssueReports
label: "Email Recipient: Issue Reports"
description: "What email address should receive issue reports"
emailRecipientNewUserAlert:
kind: panel.input.email
id: emailRecipientNewUserAlert
- name: "Notifications:NewUser"
+ name: emailRecipientNewUserAlert
label: "Email Recipient: New User Alert"
description: "What email address should receive New User Registration emails"
emailRecipientUpdate:
kind: panel.input.email
id: emailRecipientUpdate
- name: "Notifications:Update"
+ name: emailRecipientUpdate
label: "Email Recipient: Updates"
description: "What email address should receive update emails"
- notifyAdminSessionTransfer:
+ emailAllowNonuserSubscribers:
kind: panel.input.checkbox
- id: notifyAdminSessionTransfer
- name: "email:transfer"
- label: "Notify Admin on Session Transfer"
- value: false
- description: "Whether to cc admin user on session transfer by user. Requires valid admin email address."
+ id: emailAllowNonuserSubscribers
+ name: emailAllowNonuserSubscribers
+ label: "Allow Nonuser Subscribers"
+ value: true
themeManagement:
kind: panel
@@ -537,9 +621,7 @@ themeManagement:
label: Upload a theme package
description: Upload a zipped theme package for selection above.
className: themeUploader
-
-
authenticationMethods:
kind: panel.form
name: authenticationMethods
@@ -641,11 +723,19 @@ userRoles:
label: User Roles
# contents:
+
registrationOptions:
kind: panel.form
name: registrationOptions
label: Registration Options
contents:
+ requireLogin:
+ kind: panel.input.checkbox
+ id: requireLogin
+ name: requireLogin
+ label: "Require User?"
+ value: true
+ disabled: true
requireEmailVerificationToRegister:
kind: panel.input.checkbox
id: requireEmailVerificationToRegister
@@ -667,7 +757,7 @@ registrationOptions:
autoEnableUserRegistration:
kind: panel.input.checkbox
id: autoEnableUserRegistration
- name: autoEnableUserRegistration
+ name: userRegistration
label: "Auto-enable User Registration?"
value: false
allowUserCommentsOnRegistration:
@@ -676,18 +766,17 @@ registrationOptions:
name: allowUserCommentsOnRegistration
label: "Allow User Comments on Registration?"
value: true
- restrictAccessToUserList:
+ restrictUserListAccessToAdmins:
kind: panel.input.checkbox
- id: restrictAccessToUserList
- name: restrictAccessToUserList
- label: "Restrict Access to User List?"
+ id: restrictUserListAccessToAdmins
+ name: restrictUserListAccessToAdmins
+ label: "Restrict User List Access To Admins?"
value: true
dataReporting:
kind: panel.form
name: dataReporting
label: Data Reporting
- group: manageData
contents:
enableAdvancedSearch:
kind: panel.input.checkbox
@@ -696,10 +785,128 @@ dataReporting:
label: "Enable Advanced Search"
value: true
+manageDataTypes:
+ kind: panel.form
+ name: manageDataTypes
+ label: Manage Data Types
+ method: POST
+ action: /xapi/siteConfig/batch
+ load:
+ lookup: XNAT.data.siteConfig
+ contentType: json
+ contents:
+ displayNameForGenericImageSessionSingular:
+ kind: panel.input.text
+ id: displayNameForGenericImageSessionSingular
+ name: displayNameForGenericImageSession.singular
+ label: "Singular Display Name For Generic Image Session Singular"
+ value: "Session"
+ displayNameForGenericImageSessionPlural:
+ kind: panel.input.text
+ id: displayNameForGenericImageSessionPlural
+ name: displayNameForGenericImageSession.plural
+ label: "Plural Display Name For Generic Image Session Singular"
+ value: "Sessions"
+
+anonymization:
+ kind: panel.form
+ name: Anonymization
+ label: "Anonymization Script (Site Wide)"
+ contents:
+ enableSitewideAnonymizationScript:
+ kind: panel.input.checkbox
+ id: enableSitewideAnonymizationScript
+ name: enableSitewideAnonymizationScript
+ label: "Enable Site-wide Anonymization Script"
+ value: true
+ editAnonymzationScript:
+ kind: panel.input.text #textarea
+ id: editAnonymzationScript
+ name: editAnonymzationScript
+ label: "Edit Anonymzation Script"
+ value: true
+
+seriesImportFilter:
+ kind: panel.form
+ name: seriesImportFilter
+ label: "Series Import Filter"
+ contents:
+ enableSitewideSeriesImportFilter:
+ kind: panel.input.checkbox
+ id: enableSitewideSeriesImportFilter
+ name: enableSitewideSeriesImportFilter
+ label: "Enable Site-wide Series Import Filter"
+ value: false
+ filterMode:
+ kind: panel.input.checkbox
+ id: filterMode
+ name: filterMode
+ label: Filter Mode
+ value: false
+ seriesImportFilter:
+ kind: panel.input.text #textarea
+ id: seriesImportFilter
+ name: seriesImportFilter
+ label: "Edit Series Import Filter"
+
+sessionUploadMethod:
+ kind: panel.form
+ name: sessionUploadMethod
+ label: "Session Upload Method"
+ contents:
+ selectUploadMethod:
+ kind: panel.select.single
+ id: selectUploadMethod
+ name: selectUploadMethod
+ label: "Session Upload Method"
+# options: # don't know where to populate this from
+# http:
+# label: http
+# value: http
+# https:
+# label: https
+# value: https
+ showApplet:
+ kind: panel.input.checkbox
+ id: showApplet
+ name: showApplet
+ label: Show Applet
+ value: false
+ enableProjectAppletScript:
+ kind: panel.input.checkbox
+ id: enableProjectAppletScript
+ name: enableProjectAppletScript
+ label: Enable Project Applet Script
+ value: false
+ appletScript:
+ kind: panel.input.text #textarea
+ id: appletScript
+ name: appletScript
+ label: "Applet Script"
+ sessionXmlRebuilderRepeat:
+ kind: panel.input.number
+ id: sessionXmlRebuilderRepeat
+ name: sessionXmlRebuilderRepeat
+ label: Session Xml Rebuilder Repeat
+ value: 60000
+ sessionXmlRebuilderInterval:
+ kind: panel.input.number
+ id: sessionXmlRebuilderInterval
+ name: sessionXmlRebuilderInterval
+ label: Session Xml Rebuilder Interval
+ value: 5
+
+
dicomScpReceivers:
kind: panel.form
name: dicomScpReceivers
label: DICOM SCP Receivers
+ method: POST
+ action: /xapi/dicomscp
+ load:
+ url: /xapi/dicomscp
+# prop: # Not set, so should get the root object
+ contentType: json
contents:
enableDicomReceiver:
kind: panel.input.checkbox
@@ -714,9 +921,12 @@ dicomScpReceivers:
html: "Caution: Changes to this setting will take effect immediately. Before disabling the receiver, verify that there are no transmissions currently in progress."
style:
fontWeight: bold
- # hidden form element...
- # enableDicomReceiver.property.changed.listener
- # org.nrg.dcm.DicomSCPSiteConfigurationListener
+ enableDicomReceiverPropertyChangedListener: # Should this be a hidden form element??
+ kind: panel.input.text
+ id: enableDicomReceiverPropertyChangedListener
+ name: enableDicomReceiverPropertyChangedListener # Should this be "enableDicomReceiver.property.changed.listener"
+ label: "Enable Dicom Receiver Property Changed Listener"
+ value: "org.nrg.dcm.DicomSCPSiteConfigurationListener"
dicomHost:
kind: panel.input.text
id: dicomHost
@@ -741,12 +951,12 @@ dicomScpReceivers:
name: services.dicom.scp.aetitle
label: Default DICOM Receiver
description: "AE Title for default DICOM receiver"
- defaultDicomReceiverUser:
+ receivedFileUser:
kind: panel.input.text
- id: defaultDicomReceiverUser
- name: services.dicom.scp.receivedfileuser
+ id: receivedFileUser
+ name: receivedFileUser
label: "Default DICOM Receiver: User"
- value: Login failed
+ value: admin
description: "User account for default DICOM receiver"
fileSystem:
@@ -766,7 +976,37 @@ fileSystem:
${buildPath}
${pipelinePath}
${dataFolders}
+ ${zipExtensions}
+misc:
+ kind: panel.form
+ name: misc
+ label: Miscellaneous
+ method: POST
+ action: /xapi/siteConfig/batch
+ load:
+ lookup: XNAT.data.siteConfig
+ contentType: json
+ contents:
+ checksums:
+ kind: panel.input.checkbox
+ id: checksums
+ name: checksums
+ label: Checksums?
+ value: true
+ checksumsPropertyChangedListener:
+ kind: panel.input.text
+ id: checksumsPropertyChangedListener
+ name: checksums.property.changed.listener
+ label: Checksums Property Changed Listener?
+ value: org.nrg.xnat.utils.ChecksumsSiteConfigurationListener
+ scanTypeMapping:
+ kind: panel.input.checkbox
+ id: scanTypeMapping
+ name: scanTypeMapping
+ label: Scan Type Mapping?
+ value: true
+
#################################################
#### Root Site Admin Spawner Config Object ####
@@ -800,6 +1040,7 @@ siteAdmin:
${passwords}
${csrf}
${auditTrail}
+ ${securityServices}
emailServer:
kind: tab
name: emailServer
@@ -830,20 +1071,20 @@ siteAdmin:
${authenticationMethods}
${genericAuthenticationProvider}
${ldapAuthentication}
- users:
- kind: tab
- name: users
- label: Users
- group: manageAccess
- contents:
- ${users}
- userRoles:
- kind: tab
- name: userRoles
- label: User Roles
- group: manageAccess
- contents:
- ${userRoles}
+# users: # enable when users table can be re-implmented in spawner, until then use old users config?
+# kind: tab
+# name: users
+# label: Users
+# group: manageAccess
+# contents:
+# ${users}
+# userRoles: # enable when user roles table can be re-implmented in spawner, until then use old user roles config?
+# kind: tab
+# name: userRoles
+# label: User Roles
+# group: manageAccess
+# contents:
+# ${userRoles}
registrationOptions:
kind: tab
name: registrationOptions
@@ -858,6 +1099,22 @@ siteAdmin:
group: manageData
contents:
${dataReporting}
+ manageDataTypes:
+ kind: tab
+ name: manageDataTypes
+ label: Manage Data Types
+ group: manageData
+ contents:
+ ${manageDataTypes}
+ sessionUploadImportAnonymization:
+ kind: tab
+ name: sessionUploadImportAnonymization
+ label: "Session Upload, Import & Anonymization"
+ group: manageData
+ contents:
+ ${anonymization}
+ ${seriesImportFilter}
+ ${sessionUploadMethod}
dicomScpReceivers:
kind: tab
name: dicomScpReceivers
@@ -873,6 +1130,13 @@ siteAdmin:
contents:
${fileSystem}
${siteIdMain}
+ misc:
+ kind: tab
+ name: misc
+ label: Miscellaneous
+# group: misc # should show up under Other
+ contents:
+ ${misc}
###########################################
diff --git a/src/main/webapp/WEB-INF/conf/xnat-security.xml b/src/main/webapp/WEB-INF/conf/xnat-security.xml
index 0491f1fd7de06683845ad6ca0b03aec13568d29e..5ec44a3b884f4364b7b234350173e0e0a530d6c0 100644
--- a/src/main/webapp/WEB-INF/conf/xnat-security.xml
+++ b/src/main/webapp/WEB-INF/conf/xnat-security.xml
@@ -111,8 +111,6 @@
<value>/app/template/VerificationSent.vm*</value>
<value>/app/template/VerifyEmail.vm*</value>
<value>/favicon.ico</value>
- <value>/data/version</value>
- <value>/REST/version</value>
<value>/data/JSESSION</value>
<value>/REST/JSESSION</value>
<value>/data/services/auth*</value>
diff --git a/src/main/webapp/scripts/ezCalendar.js b/src/main/webapp/scripts/ezCalendar.js
index a1e0828c1b31f9d44af3ecf713cf9f9f302d5d83..b27b9acc59718dc18ba23f4b8d51f475064c73e3 100644
--- a/src/main/webapp/scripts/ezCalendar.js
+++ b/src/main/webapp/scripts/ezCalendar.js
@@ -641,7 +641,7 @@ $(function(){
var $input = $(input);
var format = XNAT.app.utils.getValueByClass($input,['iso','us','eu','euro']);
var val = $input.val();
- if (val === ('__/__/____' || '____-__-__' || '')){
+ if (val === '__/__/____' || val === '____-__-__' || val === ''){
$input.val('');
return false;
}
diff --git a/src/main/webapp/scripts/footer.js b/src/main/webapp/scripts/footer.js
index 98590d8ac31767d4ba254ddc8eeb2f76a5764c07..46c5372245ab91414e00378904aaf158b7ae1d68 100644
--- a/src/main/webapp/scripts/footer.js
+++ b/src/main/webapp/scripts/footer.js
@@ -534,9 +534,13 @@ $(function(){
// add version to title attribute of XNAT logos
if (typeof logged_in != 'undefined' && logged_in == true){
- $.get(serverRoot+'/data/version',function(data){
- XNAT_version = data.split(" ")[0];
- $('#xnat_power').find('a').attr('title','XNAT version ' + XNAT_version).after('<small>version ' + XNAT_version + '</small>');
+ $.get(serverRoot+'/xapi/siteConfig/buildInfo',function(data){
+ XNAT_version = data.version + " build: " + data.buildNumber;
+ var isNonRelease = /.*(SNAPSHOT|BETA|RC).*/.test(data.version);
+ if (isNonRelease) {
+ XNAT_version += " (" + data.commit + ")";
+ }
+ $('#xnat_power').find('a').attr('title','XNAT version ' + XNAT_version).after('<small>version ' + XNAT_version + (isNonRelease ? "<br>" + data.buildDate : "") + '</small>');
$('#header_logo').attr('title','XNAT version ' + XNAT_version);
XNAT.app.version = XNAT_version ;
});
diff --git a/src/main/webapp/scripts/timeLeft.js b/src/main/webapp/scripts/timeLeft.js
index 4239784a57d9581a21dfc0b02e51820ba1e71a33..0572060ebb0d57968a315ff6437cece0b8b9882f 100644
--- a/src/main/webapp/scripts/timeLeft.js
+++ b/src/main/webapp/scripts/timeLeft.js
@@ -180,7 +180,7 @@ if (typeof XNAT.app.timeout == 'undefined'){ XNAT.app.timeout={} }
timeout.handleOk = function () {
timeout.hideWarningDialog(timeout.warningDialog);
timeout.touchCallback.startTime = new Date().getTime();
- XNAT.xhr.get(XNAT.url.restUrl('/data/version'), timeout.touchCallback);
+ XNAT.xhr.get(XNAT.url.restUrl('/xapi/siteConfig/buildInfo'), timeout.touchCallback);
$('applet').css('visibility', 'visible');
};