SSDM-1822: educatedly guessing location of BLAST supplied with ELN

SVN: 35115

datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java

@@ -132,8 +132,7 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
         makeblastdb = blastToolDirectory + "makeblastdb";
         if (process(makeblastdb, "-version") == false)
         {
-            operationLog.error("BLAST isn't installed or property '" + BlastUtils.BLAST_TOOLS_DIRECTORY_PROPERTY 
-                    + "' hasn't been correctly specified.");
+        	BlastUtils.logMissingTools(operationLog);
             makeblastdb = null;
         }
         makembindex = blastToolDirectory + "makembindex";

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

@@ -17,10 +17,16 @@
 package ch.systemsx.cisd.openbis.dss.generic.shared.utils;
 
 import java.io.File;
+import java.nio.file.Path;
+import java.nio.file.Paths;
 import java.util.Properties;
 
+import org.apache.commons.lang.SystemUtils;
 import org.apache.log4j.Logger;
 
+import ch.systemsx.cisd.openbis.generic.shared.coreplugin.CorePluginScanner.ScannerType;
+import ch.systemsx.cisd.openbis.generic.shared.coreplugin.CorePluginsUtils;
+
 /**
  * Constants and static method about BLAST support.
  *
@@ -28,10 +34,18 @@ import org.apache.log4j.Logger;
  */
 public class BlastUtils
 {
+    private static final String BLAST_ROOT = "eln-lims/bin/blast";
+
+    private static final String LINUX = "linux/bin/";
+
+    private static final String MAC = "mac/bin/";
+
     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);
@@ -40,11 +54,36 @@ public class BlastUtils
     public static String getBLASTToolDirectory(Properties properties)
     {
         String blastToolsDirectory = properties.getProperty(BLAST_TOOLS_DIRECTORY_PROPERTY, "");
-        if (blastToolsDirectory.endsWith("/") || blastToolsDirectory.isEmpty())
+
+        if (false == blastToolsDirectory.isEmpty())
+        {
+
+            if (blastToolsDirectory.endsWith(File.separator))
+            {
+                return blastToolsDirectory;
+            }
+            return blastToolsDirectory + File.separator;
+        }
+
+        return getBestGuessBLASTToolDirectory(properties);
+    }
+
+    private static String getBestGuessBLASTToolDirectory(Properties properties)
+    {
+        String corePluginsFolder = CorePluginsUtils.getCorePluginsFolder(properties, ScannerType.DSS);
+        Path path = Paths.get(corePluginsFolder, BLAST_ROOT).toAbsolutePath();
+
+        if (false == path.toFile().exists())
         {
-            return blastToolsDirectory;
+            return "";
         }
-        return blastToolsDirectory + "/";
+
+        if (SystemUtils.IS_OS_LINUX)
+        {
+            return path.resolve(LINUX).toString() + File.separator;
+        }
+
+        return path.resolve(MAC).toString() + File.separator;
     }
 
     public static File getFile(Properties properties, String pathProperty, String defaultPath, File storeRoot)
@@ -55,7 +94,7 @@ public class BlastUtils
 
     public static void logMissingTools(Logger operationLog)
     {
-        operationLog.error("BLAST isn't installed or property '" + BLAST_TOOLS_DIRECTORY_PROPERTY 
+        operationLog.error("BLAST isn't installed or property '" + BLAST_TOOLS_DIRECTORY_PROPERTY
                 + "' hasn't been correctly specified.");
     }