From 7dce55f48022a183731abba087a16399a184f509 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 15 Jul 2014 06:39:55 +0000
Subject: [PATCH] SSDM-579: Bug fixed: Databases for data sets in trash can
have been deleted.
SVN: 32059
---
.../dss/generic/shared/utils/BlastUtils.java | 62 +++++++++++++++++++
1 file changed, 62 insertions(+)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/BlastUtils.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/BlastUtils.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/BlastUtils.java
new file mode 100644
index 00000000000..956a50f2227
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/shared/utils/BlastUtils.java
@@ -0,0 +1,62 @@
+/*
+ * 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.");
+ }
+
+}
--
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