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Commit 4fd0ae4f authored by felmer's avatar felmer
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SSDM-579: Bug fixed: Databases for data sets in trash can have been deleted. 

SVN: 32060
parent 7dce55f4
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datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/plugins/BlastDatabaseCreationMaintenanceTaskTest.java
+ 4
− 5
View file @ 4fd0ae4f
...@@ -16,9 +16,7 @@ ...@@ -16,9 +16,7 @@
package ch.systemsx.cisd.etlserver.plugins; package ch.systemsx.cisd.etlserver.plugins;
import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.BLAST_DATABASES_FOLDER_PROPERTY;
import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.BLAST_TEMP_FOLDER_PROPERTY; import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.BLAST_TEMP_FOLDER_PROPERTY;
import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.BLAST_TOOLS_DIRECTORY_PROPERTY;
import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.DATASET_TYPES_PROPERTY; import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.DATASET_TYPES_PROPERTY;
import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.FILE_TYPES_PROPERTY; import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.FILE_TYPES_PROPERTY;
import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.LAST_SEEN_DATA_SET_FILE_PROPERTY; import static ch.systemsx.cisd.etlserver.plugins.BlastDatabaseCreationMaintenanceTask.LAST_SEEN_DATA_SET_FILE_PROPERTY;
...@@ -44,6 +42,7 @@ import ch.systemsx.cisd.openbis.common.io.hierarchical_content.DefaultFileBasedH ...@@ -44,6 +42,7 @@ import ch.systemsx.cisd.openbis.common.io.hierarchical_content.DefaultFileBasedH
import ch.systemsx.cisd.openbis.dss.generic.shared.IConfigProvider; 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.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider; import ch.systemsx.cisd.openbis.dss.generic.shared.IHierarchicalContentProvider;
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.AbstractExternalData;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus; import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetArchivingStatus;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria; import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TrackingDataSetCriteria;
...@@ -219,7 +218,7 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem ...@@ -219,7 +218,7 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa, .fastq]\n" assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa, .fastq]\n"
+ INFO_PREFIX + "BLAST databases folder: " + store + "/blast-databases\n" + INFO_PREFIX + "BLAST databases folder: " + store + "/blast-databases\n"
+ INFO_PREFIX + "Temp folder '" + store + "/blast-databases/tmp' created.\n" + INFO_PREFIX + "Temp folder '" + store + "/blast-databases/tmp' created.\n"
+ ERROR_PREFIX + "BLAST isn't installed or property '" + BLAST_TOOLS_DIRECTORY_PROPERTY + ERROR_PREFIX + "BLAST isn't installed or property '" + BlastUtils.BLAST_TOOLS_DIRECTORY_PROPERTY
+ "' hasn't been correctly specified.", logRecorder.getLogContent()); + "' hasn't been correctly specified.", logRecorder.getLogContent());
context.assertIsSatisfied(); context.assertIsSatisfied();
} }
...@@ -378,10 +377,10 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem ...@@ -378,10 +377,10 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
Properties properties = new Properties(); Properties properties = new Properties();
properties.setProperty(DATASET_TYPES_PROPERTY, ".*"); properties.setProperty(DATASET_TYPES_PROPERTY, ".*");
File blastDatabasesFolder = new File(workingDirectory, "blast-dbs"); File blastDatabasesFolder = new File(workingDirectory, "blast-dbs");
properties.setProperty(BLAST_DATABASES_FOLDER_PROPERTY, blastDatabasesFolder.toString()); properties.setProperty(BlastUtils.BLAST_DATABASES_FOLDER_PROPERTY, blastDatabasesFolder.toString());
File tempFolder = new File(workingDirectory, "temp"); File tempFolder = new File(workingDirectory, "temp");
properties.setProperty(BLAST_TEMP_FOLDER_PROPERTY, tempFolder.toString()); properties.setProperty(BLAST_TEMP_FOLDER_PROPERTY, tempFolder.toString());
properties.setProperty(BLAST_TOOLS_DIRECTORY_PROPERTY, "/usr/bin/blast"); properties.setProperty(BlastUtils.BLAST_TOOLS_DIRECTORY_PROPERTY, "/usr/bin/blast");
properties.setProperty(FILE_TYPES_PROPERTY, ".txt .f"); properties.setProperty(FILE_TYPES_PROPERTY, ".txt .f");
File lastSeenFile = new File(workingDirectory, "last.txt"); File lastSeenFile = new File(workingDirectory, "last.txt");
properties.setProperty(LAST_SEEN_DATA_SET_FILE_PROPERTY, lastSeenFile.toString()); properties.setProperty(LAST_SEEN_DATA_SET_FILE_PROPERTY, lastSeenFile.toString());
......
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