From 214be38b14ccfc8d18747b3bd3e27429faab7c78 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 15 Jul 2014 06:24:01 +0000
Subject: [PATCH] SSDM-579: Bug fixed: Databases for data sets in trash can
have been deleted.
SVN: 32058
---
.../BlastDatabaseCreationMaintenanceTask.java | 67 +++++++++----------
1 file changed, 31 insertions(+), 36 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 89182f99318..1c439f46b57 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
@@ -58,7 +58,9 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IConfigProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
+import ch.systemsx.cisd.openbis.dss.generic.shared.utils.BlastUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.AbstractExternalData;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DeletedDataSet;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
/**
@@ -70,16 +72,12 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria
public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
{
static final String DATASET_TYPES_PROPERTY = "dataset-types";
- static final String BLAST_TOOLS_DIRECTORY_PROPERTY = "blast-tools-directory";
- static final String BLAST_DATABASES_FOLDER_PROPERTY = "blast-databases-folder";
static final String BLAST_TEMP_FOLDER_PROPERTY = "blast-temp-folder";
static final String LAST_SEEN_DATA_SET_FILE_PROPERTY = "last-seen-data-set-file";
static final String FILE_TYPES_PROPERTY = "file-types";
private static final String DEFAULT_LAST_SEEN_DATA_SET_FILE = "last-seen-data-set-for-BLAST-database-creation";
private static final String DEFAULT_FILE_TYPES = ".fasta .fa .fsa .fastq";
- private static final String DEFAULT_BLAST_DATABASES_FOLDER = "blast-databases";
-
private static final Logger operationLog =
LogFactory.getLogger(LogCategory.OPERATION, BlastDatabaseCreationMaintenanceTask.class);
private static final Logger machineLog =
@@ -115,12 +113,13 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
lastSeenDataSetFile = getFile(properties, LAST_SEEN_DATA_SET_FILE_PROPERTY, DEFAULT_LAST_SEEN_DATA_SET_FILE);
setUpBlastDatabasesFolder(properties);
setUpBlastTempFolder(properties);
- String blastToolDirectory = getBLASTToolDirectory(properties);
+ String blastToolDirectory = BlastUtils.getBLASTToolDirectory(properties);
makeblastdb = blastToolDirectory + "makeblastdb";
if (process(makeblastdb, "-version") == false)
{
- operationLog.error("BLAST isn't installed or property '" + BLAST_TOOLS_DIRECTORY_PROPERTY
+ operationLog.error("BLAST isn't installed or property '" + BlastUtils.BLAST_TOOLS_DIRECTORY_PROPERTY
+ "' hasn't been correctly specified.");
+ makeblastdb = null;
}
makembindex = blastToolDirectory + "makembindex";
@@ -128,7 +127,7 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
private void setUpBlastDatabasesFolder(Properties properties)
{
- blastDatabasesFolder = getFile(properties, BLAST_DATABASES_FOLDER_PROPERTY, DEFAULT_BLAST_DATABASES_FOLDER);
+ blastDatabasesFolder = BlastUtils.getBlastDatabaseFolder(properties, getConfigProvider().getStoreRoot());
operationLog.info("BLAST databases folder: " + blastDatabasesFolder);
if (blastDatabasesFolder.exists())
{
@@ -146,7 +145,7 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
}
}
}
-
+
private void setUpBlastTempFolder(Properties properties)
{
String tempFolderProperty = properties.getProperty(BLAST_TEMP_FOLDER_PROPERTY);
@@ -174,23 +173,16 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
private File getFile(Properties properties, String pathProperty, String defaultPath)
{
- String path = properties.getProperty(pathProperty);
- return path == null ? new File(getConfigProvider().getStoreRoot(), defaultPath) : new File(path);
- }
-
- private String getBLASTToolDirectory(Properties properties)
- {
- String blastToolsDirectory = properties.getProperty(BLAST_TOOLS_DIRECTORY_PROPERTY, "");
- if (blastToolsDirectory.endsWith("/") || blastToolsDirectory.isEmpty())
- {
- return blastToolsDirectory;
- }
- return blastToolsDirectory + "/";
+ return BlastUtils.getFile(properties, pathProperty, defaultPath, getConfigProvider().getStoreRoot());
}
@Override
public void execute()
{
+ if (makeblastdb == null)
+ {
+ return;
+ }
IEncapsulatedOpenBISService service = getOpenBISService();
Map<SequenceType, VirtualDatabase> virtualDatabases = loadVirtualDatabases(service);
@@ -233,13 +225,14 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
}
if (dataSetCodes.isEmpty() == false)
{
- for (AbstractExternalData dataSet : service.listDataSetsByCode(new ArrayList<String>(dataSetCodes)))
+ Set<String> deletedDataSetCodes = new HashSet<String>();
+ for (DeletedDataSet deletedDataSet : service.listDeletedDataSets(null, null))
{
- dataSetCodes.remove(dataSet.getCode());
+ deletedDataSetCodes.add(deletedDataSet.getCode());
}
for (VirtualDatabase virtualDatabase : virtualDatabases.values())
{
- virtualDatabase.removeDeletedDataSets(dataSetCodes);
+ virtualDatabase.removeDeletedDataSets(deletedDataSetCodes);
}
}
return virtualDatabases;
@@ -470,9 +463,10 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
{
for (String dataSetCode : deletedDataSets)
{
- dataSetCodes.remove(dataSetCode);
- final String databaseName = dataSetCode + postfix;
- File[] files = databaseFolder.listFiles(new FilenameFilter()
+ if (dataSetCodes.remove(dataSetCode))
+ {
+ final String databaseName = dataSetCode + postfix;
+ File[] files = databaseFolder.listFiles(new FilenameFilter()
{
@Override
public boolean accept(File dir, String name)
@@ -480,19 +474,20 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
return name.startsWith(databaseName);
}
});
- if (files != null)
- {
- boolean success = true;
- for (File file : files)
+ if (files != null)
{
- if (FileUtilities.delete(file) == false)
+ boolean success = true;
+ for (File file : files)
{
- operationLog.warn("File deletion failed: " + file);
+ if (FileUtilities.delete(file) == false)
+ {
+ operationLog.warn("File deletion failed: " + file);
+ }
+ }
+ if (success)
+ {
+ operationLog.info("BLAST database " + databaseName + " successfully deleted.");
}
- }
- if (success)
- {
- operationLog.info("BLAST database " + databaseName + " successfully deleted.");
}
}
}
--
GitLab