SSDM-579: Bug fixed: Databases for data sets in trash can have been deleted.

SVN: 32059

datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/BlastUtils.java

+/*
+ * Copyright 2014 ETH Zuerich, SIS
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *      http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.systemsx.cisd.openbis.dss.generic.shared.utils;
+
+import java.io.File;
+import java.util.Properties;
+
+import org.apache.log4j.Logger;
+
+/**
+ * Constants and static method about BLAST support.
+ *
+ * @author Franz-Josef Elmer
+ */
+public class BlastUtils
+{
+    public static final String BLAST_TOOLS_DIRECTORY_PROPERTY = "blast-tools-directory";
+    public static final String BLAST_DATABASES_FOLDER_PROPERTY = "blast-databases-folder";
+    public static final String DEFAULT_BLAST_DATABASES_FOLDER = "blast-databases";
+    
+    public static File getBlastDatabaseFolder(Properties properties, File storeRoot)
+    {
+        return getFile(properties, BLAST_DATABASES_FOLDER_PROPERTY, DEFAULT_BLAST_DATABASES_FOLDER, storeRoot);
+    }
+
+    public static String getBLASTToolDirectory(Properties properties)
+    {
+        String blastToolsDirectory = properties.getProperty(BLAST_TOOLS_DIRECTORY_PROPERTY, "");
+        if (blastToolsDirectory.endsWith("/") || blastToolsDirectory.isEmpty())
+        {
+            return blastToolsDirectory;
+        }
+        return blastToolsDirectory + "/";
+    }
+
+    public static File getFile(Properties properties, String pathProperty, String defaultPath, File storeRoot)
+    {
+        String path = properties.getProperty(pathProperty);
+        return path == null ? new File(storeRoot, defaultPath) : new File(path);
+    }
+
+    public static void logMissingTools(Logger operationLog)
+    {
+        operationLog.error("BLAST isn't installed or property '" + BLAST_TOOLS_DIRECTORY_PROPERTY 
+                + "' hasn't been correctly specified.");
+    }
+
+}