From 9519364d7a5d33b11d8099f8a7b06fb543da0cef Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 5 May 2014 11:13:56 +0000
Subject: [PATCH] SSDM-85: FASTQ example added to unit test. .fastq added to
default file types
SVN: 31455
---
.../BlastDatabaseCreationMaintenanceTask.java | 2 +-
.../BlastDatabaseCreationMaintenanceTaskTest.java | 14 +++++++-------
2 files changed, 8 insertions(+), 8 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 9066602c7e0..9238d4bd139 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
@@ -69,7 +69,7 @@ public class BlastDatabaseCreationMaintenanceTask implements IMaintenanceTask
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";
+ 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 =
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 0adc1099d30..abbf2947bd5 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
@@ -215,7 +215,7 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
maintenanceTask.setUp("", properties);
- assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa]\n"
+ assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa, .fastq]\n"
+ INFO_PREFIX + "BLAST databases folder: " + store + "/blast-databases\n"
+ INFO_PREFIX + "Temp folder '" + store + "/blast-databases/tmp' created.\n"
+ ERROR_PREFIX + "BLAST isn't installed or property '" + BLAST_TOOLS_DIRECTORY_PROPERTY
@@ -231,7 +231,7 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
maintenanceTask.setUp("BLAST databases creation", properties);
- assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa]\n"
+ assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa, .fastq]\n"
+ INFO_PREFIX + "BLAST databases folder: " + store + "/blast-databases\n"
+ INFO_PREFIX + "Temp folder '" + store + "/blast-databases/tmp' created.",
logRecorder.getLogContent());
@@ -258,7 +258,7 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
dataFolder.mkdirs();
FileUtilities.writeToFile(new File(dataSetFolder1, "fasta.txt"), ">1\nGATTACA\n");
FileUtilities.writeToFile(new File(dataSetFolder1, "fasta1.fa"), ">2\nGATTACA\nGATTACA\n");
- FileUtilities.writeToFile(new File(dataFolder, "fasta2.fa"), ">3\nIJAB\n");
+ FileUtilities.writeToFile(new File(dataFolder, "fasta2.fastq"), "@3\nIAKKATA\n+\nznhjnxzx\n");
prepareContentProvider(ds3, dataSetFolder1);
StringBuilder stringBuilder = new StringBuilder();
for (int i = 0; i < 11e5; i++)
@@ -270,7 +270,7 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
maintenanceTask.execute();
- assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa]\n"
+ assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa, .fastq]\n"
+ INFO_PREFIX + "BLAST databases folder: " + store + "/blast-databases\n"
+ INFO_PREFIX + "Temp folder '" + store + "/blast-databases/tmp' created.\n"
+ INFO_PREFIX + "Scan 4 data sets for creating BLAST databases.", logRecorder.getLogContent());
@@ -319,7 +319,7 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
maintenanceTask.execute();
- assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa]\n"
+ assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa, .fastq]\n"
+ INFO_PREFIX + "BLAST databases folder: " + store + "/blast-databases\n"
+ INFO_PREFIX + "Temp folder '" + store + "/blast-databases/tmp' created.\n"
+ INFO_PREFIX + "Scan 3 data sets for creating BLAST databases.", logRecorder.getLogContent());
@@ -348,13 +348,13 @@ public class BlastDatabaseCreationMaintenanceTaskTest extends AbstractFileSystem
RecordingMatcher<TrackingDataSetCriteria> lastSeenIdMatcher = prepareListNewerDataSet(ds1);
File dataSetFolder1 = new File(workingDirectory, "data-set-example1");
dataSetFolder1.mkdirs();
- FileUtilities.writeToFile(new File(dataSetFolder1, "fasta.fa"), ">1\nGATTACA\n");
+ FileUtilities.writeToFile(new File(dataSetFolder1, "fasta.fastq"), "@1\nGATTACA\n+\nznhjnxzx\n");
prepareContentProvider(ds1, dataSetFolder1);
maintenanceTask.setProcessSuccesses(false);
maintenanceTask.execute();
- assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa]\n"
+ assertEquals(INFO_PREFIX + "File types: [.fasta, .fa, .fsa, .fastq]\n"
+ INFO_PREFIX + "BLAST databases folder: " + store + "/blast-databases\n"
+ INFO_PREFIX + "Temp folder '" + store + "/blast-databases/tmp' created.\n"
+ INFO_PREFIX + "Scan 1 data sets for creating BLAST databases.\n"
--
GitLab