From c1c15998a6450fb6b0d971115ffa8c1ab2ad0406 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Mon, 7 Dec 2009 13:48:41 +0000
Subject: [PATCH] fix tests
SVN: 13723
---
.../bsse/cisd/dsu/dss/FlowLaneFeeder.java | 20 ++-
.../bsse/cisd/dsu/dss/FlowLaneFeederTest.java | 122 ++++++++++--------
2 files changed, 82 insertions(+), 60 deletions(-)
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
index a504d46f09e..695c247ffdc 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
@@ -76,7 +76,7 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
static final String EXTERNAL_SAMPLE_NAME_KEY = "EXTERNAL_SAMPLE_NAME";
static final String FLOW_LANE_DROP_BOX_TEMPLATE = "flow-lane-drop-box-template";
-
+
static final String SRF_INFO_PATH = "srf-info-path";
static final String ENTITY_SEPARATOR_KEY = "entity-separator";
@@ -189,7 +189,7 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
}
}
-
+
private List<String> getSRFInfo(File file)
{
if (srfInfoPathOrNull == null)
@@ -283,10 +283,7 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
flowLaneSample.getCode()
+ (externalSampleName == null ? "" : "_" + externalSampleName)
+ META_DATA_FILE_TYPE;
- // TODO : more generic solution for avoiding escape chars in file names, this is just quick and dirty
- metaFileName = metaFileName.replace("/", "_");
- metaFileName = metaFileName.replace(":", "_");
- metaFileName = metaFileName.replace("\\", "_");
+ metaFileName = asFileName(metaFileName);
FileUtilities.writeToFile(new File(flowLaneDataSet, metaFileName), builder.toString());
if (dropBox != null)
{
@@ -300,6 +297,17 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
}
}
+ // TODO : more generic solution for avoiding escape chars in file names, this is just quick and
+ // dirty
+ static String asFileName(String originalFileName)
+ {
+ String fileName = originalFileName;
+ fileName = fileName.replace("/", "_");
+ fileName = fileName.replace(":", "_");
+ fileName = fileName.replace("\\", "_");
+ return fileName;
+ }
+
private void addLine(StringBuilder builder, String key, String value)
{
builder.append(key).append('\t').append(value).append('\n');
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
index 1c52b1278a5..22eac1f49e1 100644
--- a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
@@ -52,27 +52,31 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
- *
- *
* @author Franz-Josef Elmer
*/
public class FlowLaneFeederTest extends AbstractFileSystemTestCase
{
private static final String AFFILIATION = "fmi";
+
private static final String EXTERNAL_SAMPLE_NAME = "ext23";
+
private static final String TRANSFER_DROP_BOX = "transfer-drop-box";
+
private static final Sample EXAMPLE_FLOW_CELL_SAMPLE = createFlowCellSample();
+
private static final DataSetInformation EXAMPLE_DATA_SET_INFO = createDataSetInfo();
+
private static final String SAMPLE_CODE = "fc";
+
private static final String DROP_BOX_PREFIX = "drop-box-";
-
+
private static DataSetInformation createDataSetInfo()
{
DataSetInformation dataSetInfo = new DataSetInformation();
dataSetInfo.setSampleCode(SAMPLE_CODE);
return dataSetInfo;
}
-
+
private static Sample createFlowCellSample()
{
Sample sample = new Sample();
@@ -80,13 +84,19 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
sample.setCode(SAMPLE_CODE);
return sample;
}
-
+
private FlowLaneFeeder flowLaneFeeder;
+
private Mockery context;
+
private IEncapsulatedOpenBISService service;
+
private File dropBox1;
+
private File dropBox2;
+
private File transferDropBox;
+
private File srfInfo;
@BeforeMethod
@@ -106,7 +116,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
srfInfo = new File(workingDirectory, "srfInfo");
flowLaneFeeder = createFeeder(null);
}
-
+
@AfterMethod
public void tearDown()
{
@@ -114,7 +124,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
// Otherwise one does not known which test failed.
context.assertIsSatisfied();
}
-
+
@Test
public void testMissingProperty()
{
@@ -127,19 +137,19 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
assertEquals("Given key '" + FlowLaneFeeder.FLOW_LANE_DROP_BOX_TEMPLATE
+ "' not found in properties '[]'", ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
- @Test
+
+ @Test
void testUnkownFlowLaneSample()
{
File flowCell = new File(workingDirectory, SAMPLE_CODE);
assertEquals(true, flowCell.mkdir());
FileUtilities.writeToFile(new File(flowCell, "s_3.srf"), "hello flow lane 3");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
- prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.<Sample>asList());
-
+ prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.<Sample> asList());
+
try
{
flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
@@ -148,11 +158,11 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
{
assertEquals("No flow lane sample for flow lane 3 found.", ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
- @Test
+
+ @Test
void testMissingDropBox()
{
File flowCell = new File(workingDirectory, SAMPLE_CODE);
@@ -160,8 +170,8 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
FileUtilities.writeToFile(new File(flowCell, "s_3.srf"), "hello flow lane 3");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
Sample fl = createFlowLaneSample(3);
- prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.<Sample>asList(fl));
-
+ prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.<Sample> asList(fl));
+
try
{
flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
@@ -170,16 +180,16 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
{
AssertionUtil.assertContains(DROP_BOX_PREFIX + "3", ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testUnkownFlowCell()
{
File flowCell = new File(workingDirectory, SAMPLE_CODE);
prepareLoadFlowCellSample(null);
-
+
try
{
flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
@@ -189,10 +199,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
assertEquals("Unkown flow cell sample: " + EXAMPLE_DATA_SET_INFO.getSampleIdentifier(),
ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testNotEnoughFlowLaneFiles()
{
@@ -206,7 +216,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
File originalFlowLane1 = new File(srfFolder, "s_1.srf");
FileUtilities.writeToFile(originalFlowLane1, "hello flow lane 1");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
-
+
Sample fl1 = createFlowLaneSample(1);
Sample fl2 = createFlowLaneSample(2);
prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.asList(fl1, fl2));
@@ -219,10 +229,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
{
assertEquals("Only 1 flow lane files found instead of 2.", ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testHappyCase()
{
@@ -238,17 +248,17 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
File originalFlowLane2 = new File(srfFolder, "2.srf");
FileUtilities.writeToFile(originalFlowLane2, "hello flow lane 2");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
-
+
Sample fl1 = createFlowLaneSample(1);
Sample fl2 = createFlowLaneSample(2);
prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.asList(fl1, fl2));
prepareGetProperties(Arrays.asList(fl1, fl2));
-
+
flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
-
+
checkFlowLaneDataSet(originalFlowLane1, "1");
checkFlowLaneDataSet(originalFlowLane2, "2");
-
+
File[] transferedFiles = transferDropBox.listFiles();
assertEquals(1, transferedFiles.length);
String sampleName =
@@ -258,10 +268,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
assertEquals(sampleName + "_" + EXTERNAL_SAMPLE_NAME + FlowLaneFeeder.META_DATA_FILE_TYPE,
metaFile.getName());
assertHardLinkOnSameFile(originalFlowLane2, getFile(transferedFiles[0], "2.srf"));
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testHappyCaseWithSRFInfo()
{
@@ -279,21 +289,21 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
File originalFlowLane2 = new File(srfFolder, "2.srf");
FileUtilities.writeToFile(originalFlowLane2, "hello flow lane 2");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
-
+
Sample fl1 = createFlowLaneSample(1);
Sample fl2 = createFlowLaneSample(2);
prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.asList(fl1, fl2));
prepareGetProperties(Arrays.asList(fl1, fl2));
-
+
flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
-
+
checkFlowLaneDataSet(originalFlowLane1, "1");
checkFlowLaneDataSet(originalFlowLane2, "2");
-
+
File[] transferedFiles = transferDropBox.listFiles();
assertEquals(1, transferedFiles.length);
String sampleName =
- SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + "2";
+ SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + "2";
assertEquals("G2_" + sampleName, transferedFiles[0].getName());
File metaFile = getFile(transferedFiles[0], FlowLaneFeeder.META_DATA_FILE_TYPE);
assertEquals(sampleName + "_" + EXTERNAL_SAMPLE_NAME + FlowLaneFeeder.META_DATA_FILE_TYPE,
@@ -306,10 +316,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
AssertionUtil.assertContains("file: ", lastLine);
assertEquals(8, metaData.size());
assertHardLinkOnSameFile(originalFlowLane2, getFile(transferedFiles[0], "2.srf"));
-
+
context.assertIsSatisfied();
}
-
+
@Test
public void testInvalidSRFFile()
{
@@ -319,10 +329,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
File originalFlowLane1 = new File(flowCell, "s_1.srf");
FileUtilities.writeToFile(originalFlowLane1, "hello flow lane 1");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
-
+
Sample fl1 = createFlowLaneSample(1);
prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.asList(fl1));
-
+
try
{
flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
@@ -332,10 +342,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
AssertionUtil.assertContains("Invalid SRF file", ex.getMessage());
AssertionUtil.assertContains("s_1.srf", ex.getMessage());
}
-
+
context.assertIsSatisfied();
}
-
+
private File getFile(File folder, final String fileNameExtension)
{
File[] files = folder.listFiles(new FilenameFilter()
@@ -348,7 +358,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
assertEquals(1, files.length);
return files[0];
}
-
+
@Test
public void testUndoLastOperation()
{
@@ -356,26 +366,28 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
assertEquals(2, dropBox1.list().length);
assertEquals(2, dropBox2.list().length);
assertEquals(1, transferDropBox.list().length);
-
+
flowLaneFeeder.undoLastOperation();
-
+
assertEquals(0, dropBox1.list().length);
assertEquals(0, dropBox2.list().length);
assertEquals(0, transferDropBox.list().length);
}
-
+
private void prepareLoadFlowCellSample(final Sample flowCellSample)
{
context.checking(new Expectations()
{
{
- one(service).tryGetSampleWithExperiment(EXAMPLE_DATA_SET_INFO.getSampleIdentifier());
+ one(service).tryGetSampleWithExperiment(
+ EXAMPLE_DATA_SET_INFO.getSampleIdentifier());
will(returnValue(flowCellSample));
}
});
}
-
- private void prepareListFlowLanes(final Sample flowCellSample, final List<Sample> flowLaneSamples)
+
+ private void prepareListFlowLanes(final Sample flowCellSample,
+ final List<Sample> flowLaneSamples)
{
context.checking(new Expectations()
{
@@ -440,7 +452,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
}
});
}
-
+
private void checkFlowLaneDataSet(File originalFlowLane, String flowLaneNumber)
{
File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLaneNumber);
@@ -460,6 +472,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
String metaDataFileName =
flowLaneSampleCode + (flowLaneNumber.equals("2") ? "_" + EXTERNAL_SAMPLE_NAME : "")
+ FlowLaneFeeder.META_DATA_FILE_TYPE;
+ metaDataFileName = FlowLaneFeeder.asFileName(metaDataFileName);
assertEquals(true, new File(ds, metaDataFileName).exists());
assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists());
}
@@ -471,7 +484,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
file1.setLastModified(4711000);
assertEquals(4711000, file2.lastModified());
}
-
+
private Sample createFlowLaneSample(int flowLaneNumber)
{
Sample sample = new Sample();
@@ -489,14 +502,15 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
+ flowLaneNumber);
return sample;
}
-
+
private FlowLaneFeeder createFeeder(String srfInfoScriptOrNull)
{
Properties properties = new Properties();
properties.setProperty(FlowLaneFeeder.FLOW_LANE_DROP_BOX_TEMPLATE, new File(
workingDirectory, DROP_BOX_PREFIX).getAbsolutePath()
+ "{0}");
- properties.setProperty(FlowLaneFeeder.TRANSFER_PREFIX + AFFILIATION, transferDropBox.getAbsolutePath());
+ properties.setProperty(FlowLaneFeeder.TRANSFER_PREFIX + AFFILIATION, transferDropBox
+ .getAbsolutePath());
if (srfInfoScriptOrNull != null)
{
properties.setProperty(FlowLaneFeeder.SRF_INFO_PATH, srfInfo.getAbsolutePath());
@@ -514,5 +528,5 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
}
return new FlowLaneFeeder(properties, service);
}
-
+
}
--
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