From c732cf5558538c8926176e8e94aa90ffd1e36edf Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Thu, 17 Jul 2014 06:14:11 +0000
Subject: [PATCH] SSDM-579 Bug fixed: File type of protein virtual database was
'.nal' instead of 'pal'.
SVN: 32095
---
.../plugins/BlastDatabaseCreationMaintenanceTask.java | 8 +++++---
.../plugins/BlastDatabaseCreationMaintenanceTaskTest.java | 2 +-
2 files changed, 6 insertions(+), 4 deletions(-)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java
index f62700b9e03..c4eab24b62f 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTask.java
@@ -421,13 +421,15 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
private final String postfix;
private final File databaseFile;
private final Set<String> dataSetCodes = new LinkedHashSet<String>();
+ private final String virtualDatabaseFileType;
VirtualDatabase(File databaseFolder, SequenceType sequenceType)
{
this.databaseFolder = databaseFolder;
dbtype = sequenceType.toString().toLowerCase();
postfix = "-" + dbtype;
- databaseFile = new File(databaseFolder, "all-" + dbtype + ".nal");
+ virtualDatabaseFileType = sequenceType == SequenceType.NUCL ? ".nal" : ".pal";
+ databaseFile = new File(databaseFolder, "all-" + dbtype + virtualDatabaseFileType);
if (databaseFile.isFile())
{
List<String> lines = FileUtilities.loadToStringList(databaseFile);
@@ -500,8 +502,8 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
void save()
{
- File allDatabaseFile = new File(databaseFolder, "all-" + dbtype + ".nal");
- File newAllDatabaseFile = new File(databaseFolder, "all-" + dbtype + ".nal.new");
+ File allDatabaseFile = new File(databaseFolder, "all-" + dbtype + virtualDatabaseFileType);
+ File newAllDatabaseFile = new File(databaseFolder, "all-" + dbtype + virtualDatabaseFileType + ".new");
if (dataSetCodes.isEmpty())
{
if (allDatabaseFile.exists())
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTaskTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTaskTest.java
index 51e4c2793a3..dae04dc8639 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTaskTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTaskTest.java
@@ -286,7 +286,7 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
assertEquals("TITLE all-nucl\nDBLIST DS-3-nucl",
FileUtilities.loadToString(new File(store, "blast-databases/all-nucl.nal")).trim());
assertEquals("TITLE all-prot\nDBLIST DS-3-prot",
- FileUtilities.loadToString(new File(store, "blast-databases/all-prot.nal")).trim());
+ FileUtilities.loadToString(new File(store, "blast-databases/all-prot.pal")).trim());
assertEquals("[]", Arrays.asList(new File(store, "blast-databases/tmp").listFiles()).toString());
assertEquals(0L, lastSeenIdMatcher.recordedObject().getLastSeenDataSetId());
context.assertIsSatisfied();
--
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