From 2a2737e03ce5c5cd0e30ec9eac3715f34180e1e4 Mon Sep 17 00:00:00 2001
From: Rick Herrick <jrherrick@wustl.edu>
Date: Thu, 21 Jul 2016 18:39:19 -0500
Subject: [PATCH] XNAT-2429 Workaround for weird error where
XnatRestletExtensions beans aren't being loaded by
ApplicationContext.getBeansOfType().
---
build.gradle | 2 +-
.../xnat/configuration/ApplicationConfig.java | 2 +-
.../org/nrg/xnat/configuration/OrmConfig.java | 5 +-
.../tasks/SystemPathVerification.java | 79 ++++++++++---------
.../org/nrg/xnat/restlet/XNATApplication.java | 19 +++--
5 files changed, 61 insertions(+), 46 deletions(-)
diff --git a/build.gradle b/build.gradle
index 4f42c9e0..ec3573df 100644
--- a/build.gradle
+++ b/build.gradle
@@ -1,7 +1,7 @@
def vXnat = '1.7.0-SNAPSHOT'
def vXnatPipeline = vXnat
def vXImgView = '1.0.0-SNAPSHOT'
-def vSpring = '4.2.5.RELEASE'
+def vSpring = '4.2.7.RELEASE'
def vSpringSecurity = '4.0.4.RELEASE'
def vSwagger = '2.4.0'
def vHibernate = '4.3.11.Final'
diff --git a/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java b/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
index 01aaf589..f618b49c 100644
--- a/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/ApplicationConfig.java
@@ -98,7 +98,7 @@ public class ApplicationConfig {
}
@Bean
- public XnatRestletExtensions xnatRestletExtensions() {
+ public XnatRestletExtensions defaultXnatRestletExtensions() {
return new XnatRestletExtensions(new HashSet<>(Arrays.asList(new String[] {"org.nrg.xnat.restlet.extensions"})));
}
diff --git a/src/main/java/org/nrg/xnat/configuration/OrmConfig.java b/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
index a8025ac3..fd4aa23e 100644
--- a/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
+++ b/src/main/java/org/nrg/xnat/configuration/OrmConfig.java
@@ -26,6 +26,9 @@ import java.util.Properties;
@Configuration
@EnableTransactionManagement(proxyTargetClass = true)
public class OrmConfig {
+
+ public static final String XNAT_ENTITIES_PACKAGES = "META-INF/xnat/entities/**/*-entity-packages.txt";
+
@Bean
public ImprovedNamingStrategy namingStrategy() {
return new PrefixedTableNamingStrategy("xhbm");
@@ -61,7 +64,7 @@ public class OrmConfig {
@Bean
public LocalSessionFactoryBean sessionFactory(final Environment environment, final DataSource dataSource) throws NrgServiceException {
try {
- final AggregatedAnnotationSessionFactoryBean bean = new AggregatedAnnotationSessionFactoryBean();
+ final AggregatedAnnotationSessionFactoryBean bean = new AggregatedAnnotationSessionFactoryBean(XNAT_ENTITIES_PACKAGES);
bean.setDataSource(dataSource);
bean.setCacheRegionFactory(regionFactory(environment));
bean.setHibernateProperties(hibernateProperties(environment).getObject());
diff --git a/src/main/java/org/nrg/xnat/initialization/tasks/SystemPathVerification.java b/src/main/java/org/nrg/xnat/initialization/tasks/SystemPathVerification.java
index 1048f2b6..ecdf887e 100644
--- a/src/main/java/org/nrg/xnat/initialization/tasks/SystemPathVerification.java
+++ b/src/main/java/org/nrg/xnat/initialization/tasks/SystemPathVerification.java
@@ -13,16 +13,15 @@ package org.nrg.xnat.initialization.tasks;
import org.nrg.mail.services.MailService;
import org.nrg.xdat.preferences.SiteConfigPreferences;
+import org.nrg.xnat.services.XnatAppInfo;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
-import org.springframework.context.annotation.Lazy;
import org.springframework.dao.DataAccessException;
import org.springframework.jdbc.core.JdbcTemplate;
import org.springframework.jdbc.core.ResultSetExtractor;
import org.springframework.stereotype.Component;
-import javax.inject.Inject;
import javax.mail.MessagingException;
import java.io.File;
import java.sql.ResultSet;
@@ -33,52 +32,62 @@ import java.util.Map;
@Component
public class SystemPathVerification extends AbstractInitializingTask {
+ @Autowired
+ public SystemPathVerification(final JdbcTemplate template, final MailService mailService, final SiteConfigPreferences config, final XnatAppInfo appInfo) {
+ _template = template;
+ _mailService = mailService;
+ _config = config;
+ _appInfo = appInfo;
+ }
+
@Override
public String getTaskName() {
return "System Path Verification";
}
- private final static ArrayList<String> pathErrors = new ArrayList<>();
- public static String pathErrorWarning = null;
+ private final static ArrayList<String> pathErrors = new ArrayList<>();
+ public static String pathErrorWarning = null;
@Override
public void run() {
- try {
- validatePath(_config.getArchivePath(), "Archive", true);
- validatePath(_config.getCachePath(), "Archive", false);
- validatePath(_config.getPipelinePath(), "Archive", false);
- validatePath(_config.getPrearchivePath(), "Archive", false);
+ if (_appInfo.isInitialized()) {
+ try {
+ validatePath(_config.getArchivePath(), "Archive", true);
+ validatePath(_config.getCachePath(), "Archive", false);
+ validatePath(_config.getPipelinePath(), "Archive", false);
+ validatePath(_config.getPrearchivePath(), "Archive", false);
- final ProjectExtractor pe = new ProjectExtractor();
- final Map<String, String> projects = _template.query("SELECT id, name FROM xnat_projectdata", pe);
- if(pathErrors.size() > 0) {
- // Send warning email to admin and issue browser notification
- notifyOfPathErrors(projects.size());
- } else {
- _config.setPathErrorWarning("");
+ final ProjectExtractor pe = new ProjectExtractor();
+ final Map<String, String> projects = _template.query("SELECT id, name FROM xnat_projectdata", pe);
+ if (pathErrors.size() > 0) {
+ // Send warning email to admin and issue browser notification
+ notifyOfPathErrors(projects.size());
+ } else {
+ _config.setPathErrorWarning("");
+ }
+ complete();
+ } catch (SQLException e) {
+ logger.error("An error occurred trying to retrieve the values for the system paths.", e);
}
- complete();
- } catch (Exception e) {
- logger.error("", e);
}
}
private boolean validatePath(final String path, final String displayName, final boolean checkForFiles) throws SQLException {
File filePath = new File(path);
if (!filePath.exists()) {
- pathErrors.add(displayName+" path \""+path+"\" does not exist.");
+ pathErrors.add(displayName + " path \"" + path + "\" does not exist.");
return false;
- } else if (!filePath.isDirectory()){
- pathErrors.add(displayName+" path \""+path+"\" is not a directory.");
+ } else if (!filePath.isDirectory()) {
+ pathErrors.add(displayName + " path \"" + path + "\" is not a directory.");
return false;
} else if (checkForFiles) {
File[] files = filePath.listFiles();
final String noFiles = displayName + " files do not exist under \"" + path + "\".";
- if(files == null) {
+ if (files == null) {
pathErrors.add(noFiles);
return false;
}
- if(files.length < 1) {
+ if (files.length < 1) {
pathErrors.add(noFiles);
return false;
}
@@ -98,12 +107,12 @@ public class SystemPathVerification extends AbstractInitializingTask {
}
private void notifyOfPathErrors(int numProjects) {
- if(numProjects > 0) {
+ if (numProjects > 0) {
int i = 1;
String adminEmail = _config.getAdminEmail();
String sysName = _config.getSiteId();
String emailSubj = sysName + " " + this.getTaskName() + " Failure";
- StringBuffer sb = new StringBuffer();
+ StringBuilder sb = new StringBuilder();
String singPlurl = " has";
if (numProjects > 1) {
singPlurl = "s have";
@@ -117,8 +126,8 @@ public class SystemPathVerification extends AbstractInitializingTask {
sb.append(". ");
sb.append(err);
}
- _config.setPathErrorWarning(sb.toString().replace("\n","<br>"));
- pathErrorWarning = sb.insert(0, emailSubj+": ").toString();
+ _config.setPathErrorWarning(sb.toString().replace("\n", "<br>"));
+ pathErrorWarning = sb.insert(0, emailSubj + ": ").toString();
logger.error(pathErrorWarning);
try {
_mailService.sendHtmlMessage(adminEmail, adminEmail, emailSubj, pathErrorWarning);
@@ -130,14 +139,8 @@ public class SystemPathVerification extends AbstractInitializingTask {
private static Logger logger = LoggerFactory.getLogger(SystemPathVerification.class);
- @Autowired
- @Lazy
- private JdbcTemplate _template;
-
- @Inject
- private MailService _mailService;
-
- @Autowired
- @Lazy
- private SiteConfigPreferences _config;
+ private final JdbcTemplate _template;
+ private final MailService _mailService;
+ private final SiteConfigPreferences _config;
+ private final XnatAppInfo _appInfo;
}
diff --git a/src/main/java/org/nrg/xnat/restlet/XNATApplication.java b/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
index f297f018..fc54abf4 100755
--- a/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
+++ b/src/main/java/org/nrg/xnat/restlet/XNATApplication.java
@@ -366,22 +366,31 @@ public class XNATApplication extends Application {
*/
@SuppressWarnings("unchecked")
private List<Class<? extends Resource>> addExtensionRoutes(Router router) {
- Set<String> packages = new HashSet<>();
+ final Set<String> packages = new HashSet<>();
final Map<String, XnatRestletExtensions> pkgLists = XDAT.getContextService().getBeansOfType(XnatRestletExtensions.class);
+ if (pkgLists.size() == 0) {
+ final XnatRestletExtensions extensions = XDAT.getContextService().getBean("defaultXnatRestletExtensions", XnatRestletExtensions.class);
+ if (extensions != null) {
+ pkgLists.put("defaultXnatRestletExtensions", extensions);
+ }
+ }
for (XnatRestletExtensions pkgList : pkgLists.values()) {
packages.addAll(pkgList);
}
+ if (packages.size() == 0) {
+ packages.add("org.nrg.xnat.restlet.extensions");
+ }
- List<Class<? extends Resource>> classes = new ArrayList<>();
- List<Class<? extends Resource>> publicClasses = new ArrayList<>();
+ final List<Class<? extends Resource>> classes = new ArrayList<>();
+ final List<Class<? extends Resource>> publicClasses = new ArrayList<>();
- for (String pkg : packages) {
+ for (final String pkg : packages) {
try {
final List<Class<?>> classesForPackage = Reflection.getClassesForPackage(pkg);
if (_log.isDebugEnabled()) {
_log.debug("Found " + classesForPackage.size() + " classes for package: " + pkg);
}
- for (Class<?> clazz : classesForPackage) {
+ for (final Class<?> clazz : classesForPackage) {
if (Resource.class.isAssignableFrom(clazz)) {
if (_log.isDebugEnabled()) {
_log.debug("Found resource class: " + clazz.getName());
--
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