Merge branch '5.10.0'

pom.xml

@@ -4,7 +4,7 @@
     <groupId>org.jbei</groupId>
     <artifactId>ice</artifactId>
     <packaging>war</packaging>
-    <version>5.9.6</version>
+    <version>5.10.0</version>
     <name>ice</name>
     <description>Inventory of Composable Elements (ICE) for Synthetic Biology</description>
     <repositories>

src/main/java/org/jbei/ice/ApplicationInitialize.java

@@ -1,12 +1,27 @@
 package org.jbei.ice;
 
+import org.apache.commons.lang3.StringUtils;
 import org.jbei.ice.lib.account.AccountController;
 import org.jbei.ice.lib.common.logging.Logger;
 import org.jbei.ice.lib.config.ConfigurationSettings;
+import org.jbei.ice.lib.dto.ConfigurationKey;
 import org.jbei.ice.lib.entry.sequence.annotation.AutoAnnotationBlastDbBuildTask;
 import org.jbei.ice.lib.executor.IceExecutorService;
 import org.jbei.ice.lib.group.GroupController;
 import org.jbei.ice.lib.search.blast.RebuildBlastIndexTask;
+import org.jbei.ice.storage.DAOFactory;
+import org.jbei.ice.storage.hibernate.DbType;
+import org.jbei.ice.storage.hibernate.HibernateConfiguration;
+import org.jbei.ice.storage.hibernate.dao.ConfigurationDAO;
+import org.jbei.ice.storage.model.ConfigurationModel;
+
+import java.io.FileInputStream;
+import java.io.IOException;
+import java.nio.file.Files;
+import java.nio.file.Path;
+import java.nio.file.Paths;
+import java.util.Iterator;
+import java.util.Properties;
 
 /**
  * Responsible for initializing the ICE application
@@ -16,11 +31,126 @@
  */
 public class ApplicationInitialize {
 
+    private static final String SERVER_PROPERTY_NAME = "ice-server.properties";
+
     /**
      * Responsible for initializing the system and checking for the existence of needed
      * data (such as settings) and creating as needed
+     *
+     * @return a valid data directory path or null if none could be detected
      */
-    public static void startUp() {
+    public static Path configure() {
+        try {
+            // get or initialize data directory
+            Path dataDirectory = initializeDataDirectory();
+            if (dataDirectory == null || !Files.exists(dataDirectory))
+                return null;
+
+            // check if there is a ice-server.properties in the config directory inside the data directory
+            // and use it to connect to the database if so
+            if (Files.exists(Paths.get(dataDirectory.toString(), "config", SERVER_PROPERTY_NAME))) {
+                loadServerProperties(dataDirectory);
+            } else {
+                // todo : do not initialize hibernate unless "diva-server.properties is available
+                // todo : this will force a redirect on the ui and let user create/select a supported database
+
+                // unless there is already a db directory (check if using for built-in database)
+                // since using the built in doesn't require a config file
+                Path dbFolder = Paths.get(dataDirectory.toString(), "db");
+                if (Files.exists(dbFolder) && Files.isDirectory(dbFolder)) {
+                    // check if there is a database with the name diva-h2db
+                    Iterator<Path> files = Files.list(dbFolder).iterator();
+                    if (files.hasNext()) {
+                        Path file = files.next();
+                        String fileName = file.getFileName().toString();
+                        if (fileName.endsWith(".db") && fileName.startsWith("ice-h2db")) {
+                            HibernateConfiguration.initialize(DbType.H2DB, null, dataDirectory);
+                            return dataDirectory;
+                        } else {
+                            // db folder located but no database
+                            return null;
+                        }
+                    }
+                } else if (Files.isWritable(dataDirectory)) {
+                    // create the db directory for the file database
+                    Files.createDirectory(dbFolder);
+                    // todo : create database config file template
+                    // todo : create ldap-config.properties.template
+                    HibernateConfiguration.initialize(DbType.H2DB, null, dataDirectory); // this creates a directory "/db"
+                }
+            }
+
+            return dataDirectory;
+        } catch (Exception e) {
+            Logger.error(e);
+            throw new RuntimeException(e);
+        }
+    }
+
+    // this should not create a home directory
+    private static Path initializeDataDirectory() {
+        // check environ variable
+        String propertyHome = System.getenv("ICE_DATA_HOME");
+        Path iceHome;
+
+        if (StringUtils.isBlank(propertyHome)) {
+            // check system property (-D in startup script)
+            propertyHome = System.getProperty("ICE_DATA_HOME");
+
+            // still nothing, check home directory
+            if (StringUtils.isBlank(propertyHome)) {
+                String userHome = System.getProperty("user.home");
+                iceHome = Paths.get(userHome, ".ICEData");
+                if (!Files.exists(iceHome)) {
+                    // create home directory
+                    try {
+                        if (Files.isWritable(Paths.get(userHome)))
+                            return Files.createDirectory(iceHome);
+                        else
+                            return null;
+                    } catch (IOException e) {
+                        Logger.error(e);
+                        return null;
+                    }
+                }
+            } else {
+                iceHome = Paths.get(propertyHome);
+            }
+        } else {
+            iceHome = Paths.get(propertyHome);
+        }
+
+        Logger.info("Using ICE data directory: " + iceHome);
+        return iceHome;
+    }
+
+    // initialize the database using the database configuration
+    private static void loadServerProperties(Path dataDirectory) throws IOException {
+        Path serverPropertiesPath = Paths.get(dataDirectory.toString(), "config", SERVER_PROPERTY_NAME);
+        Properties properties = new Properties();
+        properties.load(new FileInputStream(serverPropertiesPath.toFile()));
+
+        Logger.info("Loading server properties from " + serverPropertiesPath);
+
+        // get type of data base
+        String dbTypeString = properties.getProperty("connectionType");
+        DbType type;
+        if (StringUtils.isBlank(dbTypeString)) {
+            Logger.error("Property \"connectionType\" not found. Defaulting to value of " + DbType.POSTGRESQL);
+            type = DbType.POSTGRESQL;
+        } else {
+            type = DbType.valueOf(dbTypeString.toUpperCase());
+        }
+
+        // get type of database etc
+        HibernateConfiguration.initialize(type, properties, dataDirectory);
+    }
+
+    /**
+     * Responsible for initializing the system and checking for the existence of needed
+     * data (such as settings) and creating as needed
+     */
+    public static void startUp(Path dataDirectory) {
         IceExecutorService.getInstance().startService();
 
         // check for and create public group
@@ -35,6 +165,9 @@ public static void startUp() {
         ConfigurationSettings settings = new ConfigurationSettings();
         settings.initPropertyValues();
 
+        // check data directory
+        checkDataDirectory(dataDirectory);
+
         try {
             // check blast database exists and build if it doesn't
             RebuildBlastIndexTask task = new RebuildBlastIndexTask();
@@ -46,4 +179,23 @@ public static void startUp() {
             Logger.error(e);
         }
     }
+
+    private static void checkDataDirectory(Path dataDirectory) {
+        ConfigurationSettings settings = new ConfigurationSettings();
+        String value = settings.getPropertyValue(ConfigurationKey.DATA_DIRECTORY);
+        if (!StringUtils.isEmpty(value))
+            return;
+
+        ConfigurationDAO dao = DAOFactory.getConfigurationDAO();
+        ConfigurationModel model = dao.get(ConfigurationKey.DATA_DIRECTORY);
+        if (model == null) {
+            model = new ConfigurationModel();
+            model.setKey(ConfigurationKey.DATA_DIRECTORY.name());
+            model.setValue(dataDirectory.toString());
+            dao.create(model);
+        } else {
+            model.setValue(dataDirectory.toString());
+            dao.update(model);
+        }
+    }
 }

src/main/java/org/jbei/ice/lib/config/ConfigurationSettings.java

@@ -9,7 +9,7 @@
 import org.jbei.ice.lib.net.WoRController;
 import org.jbei.ice.storage.DAOFactory;
 import org.jbei.ice.storage.hibernate.dao.ConfigurationDAO;
-import org.jbei.ice.storage.model.Configuration;
+import org.jbei.ice.storage.model.ConfigurationModel;
 import org.rauschig.jarchivelib.Archiver;
 import org.rauschig.jarchivelib.ArchiverFactory;
 
@@ -45,14 +45,14 @@ public Setting getSystemVersion(String url) {
     }
 
     public String getPropertyValue(ConfigurationKey key) {
-        Configuration config = dao.get(key);
+        ConfigurationModel config = dao.get(key);
         if (config == null)
             return key.getDefaultValue();
         return config.getValue();
     }
 
     public Setting getPropertyValue(String key) {
-        Configuration config = dao.get(key);
+        ConfigurationModel config = dao.get(key);
         if (config == null)
             return null;
         return config.toDataTransferObject();
@@ -80,16 +80,16 @@ public List<Setting> getSampleRequestSettings(String userId) {
     }
 
     private Setting getConfigValue(ConfigurationKey key) {
-        Configuration configuration = dao.get(key);
+        ConfigurationModel configuration = dao.get(key);
         if (configuration == null)
             return new Setting(key.name(), "");
         return new Setting(configuration.getKey(), configuration.getValue());
     }
 
-    public Configuration setPropertyValue(ConfigurationKey key, String value) {
-        Configuration configuration = dao.get(key);
+    public ConfigurationModel setPropertyValue(ConfigurationKey key, String value) {
+        ConfigurationModel configuration = dao.get(key);
         if (configuration == null) {
-            configuration = new Configuration();
+            configuration = new ConfigurationModel();
             configuration.setKey(key.name());
             configuration.setValue(value);
             return dao.create(configuration);
@@ -105,7 +105,7 @@ public Setting updateSetting(String userId, Setting setting, String url) {
             throw new PermissionException("Cannot update system setting without admin privileges");
 
         ConfigurationKey key = ConfigurationKey.valueOf(setting.getKey());
-        Configuration configuration = setPropertyValue(key, setting.getValue());
+        ConfigurationModel configuration = setPropertyValue(key, setting.getValue());
 
         // check if the setting being updated is related to the web of registries
         if (key == ConfigurationKey.JOIN_WEB_OF_REGISTRIES) {
@@ -123,12 +123,12 @@ public Setting autoUpdateSetting(String userId, Setting setting) {
         if (!accountController.isAdministrator(userId))
             throw new PermissionException("Cannot auto update system setting without admin privileges");
 
-        Configuration configuration = dao.get(setting.getKey());
+        ConfigurationModel configuration = dao.get(setting.getKey());
         if (configuration == null) {
             Logger.warn("Could not retrieve setting " + setting.getKey() + ". Creating...");
             if (setting.getValue() == null)
                 setting.setValue("");
-            configuration = dao.create(new Configuration(setting.getKey(), setting.getValue()));
+            configuration = dao.create(new ConfigurationModel(setting.getKey(), setting.getValue()));
         }
 
         String osName = System.getProperty("os.name").replaceAll("\\s+", "").toLowerCase();
@@ -169,7 +169,7 @@ public Setting autoUpdateSetting(String userId, Setting setting) {
      */
     public void initPropertyValues() {
         for (ConfigurationKey key : ConfigurationKey.values()) {
-            Configuration config = dao.get(key);
+            ConfigurationModel config = dao.get(key);
             if (config == null || (config.getValue().isBlank() && !key.getDefaultValue().isEmpty())) {
                 Logger.info("Setting value for " + key.name() + " to " + key.getDefaultValue());
                 setPropertyValue(key, key.getDefaultValue());

src/main/java/org/jbei/ice/lib/config/SiteSettings.java

@@ -9,7 +9,7 @@
  */
 public class SiteSettings implements IDataTransferModel {
 
-    private String version = "5.9.6";
+    private String version = "5.10.0";
     private String assetName;
     private boolean hasLogo;
     private boolean hasLoginMessage;

src/main/java/org/jbei/ice/lib/dto/ConfigurationKey.java

@@ -11,7 +11,7 @@
  */
 public enum ConfigurationKey implements IDataTransferModel {
 
-    APPLICATION_VERSION("5.9.6"),
+    APPLICATION_VERSION("5.10.0"),
     TEMPORARY_DIRECTORY("/tmp"),
     DATA_DIRECTORY("data"),
 

src/main/java/org/jbei/ice/lib/entry/sequence/PartSequence.java

@@ -653,7 +653,7 @@ private FeaturedDNASequence getFeaturedSequence(Entry entry, boolean canEdit, bo
         FeaturedDNASequence featuredDNASequence = SequenceUtil.sequenceToDNASequence(sequence, sequenceFeatures);
         featuredDNASequence.setCanEdit(canEdit);
         featuredDNASequence.setIdentifier(entry.getPartNumber());
-        Configuration configuration = DAOFactory.getConfigurationDAO().get(ConfigurationKey.URI_PREFIX);
+        ConfigurationModel configuration = DAOFactory.getConfigurationDAO().get(ConfigurationKey.URI_PREFIX);
 
         if (configuration != null) {
             String uriPrefix = configuration.getValue();

src/main/java/org/jbei/ice/lib/executor/TaskHandler.java

@@ -1,7 +1,7 @@
 package org.jbei.ice.lib.executor;
 
 import org.jbei.ice.lib.common.logging.Logger;
-import org.jbei.ice.storage.hibernate.HibernateUtil;
+import org.jbei.ice.storage.hibernate.HibernateConfiguration;
 
 /**
  * Runnable for running tasks
@@ -20,13 +20,13 @@ class TaskHandler implements Runnable {
     public void run() {
         try {
             this.task.setStatus(TaskStatus.IN_PROGRESS);
-            HibernateUtil.beginTransaction();
+            HibernateConfiguration.beginTransaction();
             task.execute();
-            HibernateUtil.commitTransaction();
+            HibernateConfiguration.commitTransaction();
             this.task.setStatus(TaskStatus.COMPLETED);
         } catch (Throwable caught) {
             Logger.error(caught);
-            HibernateUtil.rollbackTransaction();
+            HibernateConfiguration.rollbackTransaction();
             this.task.setStatus(TaskStatus.EXCEPTION);
         }
     }

src/main/java/org/jbei/ice/lib/net/RemoteEntriesAsCSV.java

@@ -189,7 +189,7 @@ protected void writeLocalEntries(List<Long> entries, List<EntryFieldLabel> field
             return;
 
         SequenceDAO sequenceDAO = DAOFactory.getSequenceDAO();
-        Configuration configuration = DAOFactory.getConfigurationDAO().get(ConfigurationKey.URI_PREFIX);
+        ConfigurationModel configuration = DAOFactory.getConfigurationDAO().get(ConfigurationKey.URI_PREFIX);
         String thisUrl = configuration == null ? "" : configuration.getValue();
 
         for (Long id : entries) {

src/main/java/org/jbei/ice/lib/search/RebuildLuceneIndexTask.java

@@ -6,7 +6,7 @@
 import org.hibernate.search.Search;
 import org.jbei.ice.lib.common.logging.Logger;
 import org.jbei.ice.lib.executor.Task;
-import org.jbei.ice.storage.hibernate.HibernateUtil;
+import org.jbei.ice.storage.hibernate.HibernateConfiguration;
 
 /**
  * Task to rebuild lucene index
@@ -18,7 +18,7 @@ public class RebuildLuceneIndexTask extends Task {
     @Override
     public void execute() {
         Logger.info("Rebuilding lucene index in background");
-        Session session = HibernateUtil.newSession();
+        Session session = HibernateConfiguration.newSession();
         FullTextSession fullTextSession = Search.getFullTextSession(session);
         MassIndexer indexer = fullTextSession.createIndexer();
         indexer.idFetchSize(20);

src/main/java/org/jbei/ice/services/rest/AuthenticationInterceptor.java

@@ -11,7 +11,7 @@
 import org.jbei.ice.lib.common.logging.Logger;
 import org.jbei.ice.lib.dto.ConfigurationKey;
 import org.jbei.ice.lib.utils.Utils;
-import org.jbei.ice.storage.hibernate.HibernateUtil;
+import org.jbei.ice.storage.hibernate.HibernateConfiguration;
 
 import javax.annotation.Priority;
 import javax.ws.rs.Priorities;
@@ -57,10 +57,10 @@ public class AuthenticationInterceptor implements ContainerRequestFilter, Reader
         private final File directory;
         {
             // need to force-create a transaction to get the DATA_DIRECTORY config value
-            HibernateUtil.beginTransaction();
+            HibernateConfiguration.beginTransaction();
             directory = Paths.get(Utils.getConfigValue(ConfigurationKey.DATA_DIRECTORY),
                     "rest-auth").toFile();
-            HibernateUtil.commitTransaction();
+            HibernateConfiguration.commitTransaction();
         }
 
         @Override

src/main/java/org/jbei/ice/services/rest/IceRequestFilter.java

@@ -1,6 +1,6 @@
 package org.jbei.ice.services.rest;
 
-import org.jbei.ice.storage.hibernate.HibernateUtil;
+import org.jbei.ice.storage.hibernate.HibernateConfiguration;
 
 import javax.ws.rs.container.ContainerRequestContext;
 import javax.ws.rs.container.ContainerRequestFilter;
@@ -18,6 +18,6 @@ public class IceRequestFilter implements ContainerRequestFilter {
 
     @Override
     public void filter(ContainerRequestContext requestContext) {
-        HibernateUtil.beginTransaction();
+        HibernateConfiguration.beginTransaction();
     }
 }