From d24aa387599cfa2d763103f972a782f101bffb14 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Mon, 26 Oct 2009 10:22:04 +0000
Subject: [PATCH] LMS-1233, LMS-1242
SVN: 13063
---
...lowLineFeeder.java => FlowLaneFeeder.java} | 105 +++++++------
.../bsse/cisd/dsu/dss/StorageProcessor.java | 2 +-
...eederTest.java => FlowLaneFeederTest.java} | 142 ++++++++++++------
3 files changed, 148 insertions(+), 101 deletions(-)
rename deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/{FlowLineFeeder.java => FlowLaneFeeder.java} (76%)
rename deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/{FlowLineFeederTest.java => FlowLaneFeederTest.java} (73%)
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
similarity index 76%
rename from deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
rename to deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
index 6855c9a0214..7437b2861b3 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
@@ -55,39 +55,39 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
- * Post registration data set handler which makes a hard-link copy of all flow-line files
+ * Post registration data set handler which makes a hard-link copy of all flow-lane files
* to associated drop boxes.
*
* @author Franz-Josef Elmer
*/
-class FlowLineFeeder implements IPostRegistrationDatasetHandler
+class FlowLaneFeeder implements IPostRegistrationDatasetHandler
{
static final String META_DATA_FILE_TYPE = ".tsv";
static final String TRANSFER_PREFIX = "transfer.";
static final String AFFILIATION_KEY = "AFFILIATION";
static final String EXTERNAL_SAMPLE_NAME_KEY = "EXTERNAL_SAMPLE_NAME";
- static final String FLOW_LINE_DROP_BOX_TEMPLATE = "flow-line-drop-box-template";
+ static final String FLOW_LANE_DROP_BOX_TEMPLATE = "flow-lane-drop-box-template";
static final String ENTITY_SEPARATOR_KEY = "entity-separator";
static final String DEFAULT_ENTITY_SEPARATOR = "_";
static final String FILE_TYPE = ".srf";
private final static Logger operationLog =
- LogFactory.getLogger(LogCategory.OPERATION, FlowLineFeeder.class);
+ LogFactory.getLogger(LogCategory.OPERATION, FlowLaneFeeder.class);
private final IEncapsulatedOpenBISService service;
- private final MessageFormat flowLineDropBoxTemplate;
+ private final MessageFormat flowLaneDropBoxTemplate;
private final String entitySepaparator;
private final IImmutableCopier copier;
private final IFileOperations fileOperations;
private final List<File> createdFiles = new ArrayList<File>();
private final Map<String, File> transferDropBoxes = new HashMap<String, File>();
- FlowLineFeeder(Properties properties, IEncapsulatedOpenBISService service)
+ FlowLaneFeeder(Properties properties, IEncapsulatedOpenBISService service)
{
this.service = service;
- flowLineDropBoxTemplate =
+ flowLaneDropBoxTemplate =
new MessageFormat(PropertyUtils.getMandatoryProperty(properties,
- FLOW_LINE_DROP_BOX_TEMPLATE));
+ FLOW_LANE_DROP_BOX_TEMPLATE));
entitySepaparator = properties.getProperty(ENTITY_SEPARATOR_KEY, DEFAULT_ENTITY_SEPARATOR);
copier = FastRecursiveHardLinkMaker.tryCreate(TimingParameters.getDefaultParameters());
fileOperations = FileOperations.getInstance();
@@ -110,47 +110,52 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
public void handle(File originalData, DataSetInformation dataSetInformation)
{
- Map<String, Sample> flowLineSampleMap = createFlowLineSampleMap(dataSetInformation);
+ Map<String, Sample> flowLaneSampleMap = createFlowLaneSampleMap(dataSetInformation);
String flowcellID = originalData.getName();
List<File> files = new ArrayList<File>();
findFiles(originalData, files);
+ if (files.size() < flowLaneSampleMap.size())
+ {
+ throw new EnvironmentFailureException("Only " + files.size()
+ + " flow lane files found instead of " + flowLaneSampleMap.size() + ".");
+ }
for (File file : files)
{
- String flowLine = extractFlowLine(file);
- Sample flowLineSample = flowLineSampleMap.get(flowLine);
- File dropBox = createDropBoxFile(flowLine);
+ String flowLane = extractFlowLane(file);
+ Sample flowLaneSample = flowLaneSampleMap.get(flowLane);
+ File dropBox = createDropBoxFile(flowLane);
String fileName =
- flowLineSample.getGroup().getCode() + entitySepaparator + flowcellID
- + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + flowLine;
- File flowLineDataSet = new File(dropBox, fileName);
- if (flowLineDataSet.exists())
+ flowLaneSample.getGroup().getCode() + entitySepaparator + flowcellID
+ + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + flowLane;
+ File flowLaneDataSet = new File(dropBox, fileName);
+ if (flowLaneDataSet.exists())
{
- throw new EnvironmentFailureException("There is already a data set for flow line "
- + flowLine + ".");
+ throw new EnvironmentFailureException("There is already a data set for flow lane "
+ + flowLane + ".");
}
- createdFiles.add(flowLineDataSet);
- boolean success = flowLineDataSet.mkdir();
+ createdFiles.add(flowLaneDataSet);
+ boolean success = flowLaneDataSet.mkdir();
if (success == false)
{
throw new EnvironmentFailureException("Couldn't create folder '"
- + flowLineDataSet.getAbsolutePath() + "'.");
+ + flowLaneDataSet.getAbsolutePath() + "'.");
}
- createHartLink(file, flowLineDataSet);
- createMetaDataFileAndHartLinkInTransferDropBox(flowLineDataSet, flowLineSample, flowLine);
+ createHartLink(file, flowLaneDataSet);
+ createMetaDataFileAndHartLinkInTransferDropBox(flowLaneDataSet, flowLaneSample, flowLane);
File markerFile = new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName);
createdFiles.add(markerFile);
FileUtilities.writeToFile(markerFile, "");
if (operationLog.isInfoEnabled())
{
- operationLog.info("Flow line file '" + file
+ operationLog.info("Flow lane file '" + file
+ "' successfully dropped into drop box '" + dropBox
- + "' as '" + flowLineDataSet.getName() + "'.");
+ + "' as '" + flowLaneDataSet.getName() + "'.");
}
}
}
- private Map<String, Sample> createFlowLineSampleMap(DataSetInformation dataSetInformation)
+ private Map<String, Sample> createFlowLaneSampleMap(DataSetInformation dataSetInformation)
{
SampleIdentifier sampleIdentifier = dataSetInformation.getSampleIdentifier();
Sample flowCell = service.tryGetSampleWithExperiment(sampleIdentifier);
@@ -160,27 +165,27 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
}
TechId flowCellID = new TechId(flowCell.getId());
ListSampleCriteria criteria = ListSampleCriteria.createForContainer(flowCellID);
- List<Sample> flowLineSamples = service.listSamples(criteria);
- Map<String, Sample> flowLineSampleMap = new LinkedHashMap<String, Sample>();
- for (Sample flowLineSample : flowLineSamples)
+ List<Sample> flowLaneSamples = service.listSamples(criteria);
+ Map<String, Sample> flowLaneSampleMap = new LinkedHashMap<String, Sample>();
+ for (Sample flowLaneSample : flowLaneSamples)
{
- flowLineSampleMap.put(flowLineSample.getSubCode(), flowLineSample);
+ flowLaneSampleMap.put(flowLaneSample.getSubCode(), flowLaneSample);
}
- return flowLineSampleMap;
+ return flowLaneSampleMap;
}
- private void createMetaDataFileAndHartLinkInTransferDropBox(File flowLineDataSet,
- Sample flowLineSample, String flowLine)
+ private void createMetaDataFileAndHartLinkInTransferDropBox(File flowLaneDataSet,
+ Sample flowLaneSample, String flowLane)
{
- if (flowLineSample == null)
+ if (flowLaneSample == null)
{
- throw new UserFailureException("No flow line sample for flow line " + flowLine + " exists");
+ throw new UserFailureException("No flow lane sample for flow lane " + flowLane + " exists");
}
StringBuilder builder = new StringBuilder();
- addLine(builder, "Parent", flowLineSample.getGeneratedFrom().getIdentifier());
- addLine(builder, "Code", flowLineSample.getCode());
- addLine(builder, "Contact Person Email", flowLineSample.getRegistrator().getEmail());
- SampleIdentifier identifier = SampleIdentifierFactory.parse(flowLineSample.getIdentifier());
+ addLine(builder, "Parent", flowLaneSample.getGeneratedFrom().getIdentifier());
+ addLine(builder, "Code", flowLaneSample.getCode());
+ addLine(builder, "Contact Person Email", flowLaneSample.getRegistrator().getEmail());
+ SampleIdentifier identifier = SampleIdentifierFactory.parse(flowLaneSample.getIdentifier());
IEntityProperty[] properties = service.getPropertiesOfTopSampleRegisteredFor(identifier);
File dropBox = null;
String externalSampleName = null;
@@ -200,16 +205,16 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
}
}
String metaFileName =
- flowLineSample.getCode()
+ flowLaneSample.getCode()
+ (externalSampleName == null ? "" : "_" + externalSampleName) + META_DATA_FILE_TYPE;
- FileUtilities.writeToFile(new File(flowLineDataSet, metaFileName), builder.toString());
+ FileUtilities.writeToFile(new File(flowLaneDataSet, metaFileName), builder.toString());
if (dropBox != null)
{
- createHartLink(flowLineDataSet, dropBox);
- createdFiles.add(new File(dropBox, flowLineDataSet.getName()));
+ createHartLink(flowLaneDataSet, dropBox);
+ createdFiles.add(new File(dropBox, flowLaneDataSet.getName()));
if (operationLog.isInfoEnabled())
{
- operationLog.info("Flow line data set '" + flowLineDataSet.getName()
+ operationLog.info("Flow lane data set '" + flowLaneDataSet.getName()
+ "' successfully transfered to drop box '" + dropBox + "'");
}
}
@@ -232,9 +237,9 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
}
}
- private File createDropBoxFile(String flowLine)
+ private File createDropBoxFile(String flowLane)
{
- File dropBox = new File(flowLineDropBoxTemplate.format(new Object[] {flowLine}));
+ File dropBox = new File(flowLaneDropBoxTemplate.format(new Object[] {flowLane}));
if (dropBox.exists() == false)
{
throw new ConfigurationFailureException("Drop box '" + dropBox + "' does not exist.");
@@ -246,17 +251,17 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
return dropBox;
}
- private String extractFlowLine(File file)
+ private String extractFlowLane(File file)
{
String name = file.getName();
String nameWithoutType = name.substring(0, name.lastIndexOf('.'));
int lastIndexOfUnderScore = nameWithoutType.lastIndexOf('_');
- String flowLine = nameWithoutType;
+ String flowLane = nameWithoutType;
if (lastIndexOfUnderScore >= 0)
{
- flowLine = nameWithoutType.substring(lastIndexOfUnderScore + 1);
+ flowLane = nameWithoutType.substring(lastIndexOfUnderScore + 1);
}
- return flowLine;
+ return flowLane;
}
private void findFiles(File file, List<File> files)
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/StorageProcessor.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/StorageProcessor.java
index d220b5a0934..88a841a840a 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/StorageProcessor.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/StorageProcessor.java
@@ -32,7 +32,7 @@ public class StorageProcessor extends DelegatingStorageProcessorWithDropbox
{
public StorageProcessor(Properties properties)
{
- super(properties, new FlowLineFeeder(properties, ServiceProvider.getOpenBISService()));
+ super(properties, new FlowLaneFeeder(properties, ServiceProvider.getOpenBISService()));
}
}
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
similarity index 73%
rename from deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
rename to deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
index 875f6f50247..d785a3a8f47 100644
--- a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
@@ -34,6 +34,7 @@ import org.testng.annotations.Test;
import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.Constants;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.logging.LogInitializer;
import ch.systemsx.cisd.common.test.AssertionUtil;
@@ -54,7 +55,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
*
* @author Franz-Josef Elmer
*/
-public class FlowLineFeederTest extends AbstractFileSystemTestCase
+public class FlowLaneFeederTest extends AbstractFileSystemTestCase
{
private static final String AFFILIATION = "fmi";
private static final String EXTERNAL_SAMPLE_NAME = "ext23";
@@ -79,7 +80,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
return sample;
}
- private FlowLineFeeder flowLineFeeder;
+ private FlowLaneFeeder flowLaneFeeder;
private Mockery context;
private IEncapsulatedOpenBISService service;
private File dropBox1;
@@ -102,11 +103,11 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
transferDropBox = new File(workingDirectory, TRANSFER_DROP_BOX);
assertEquals(true, transferDropBox.mkdirs());
Properties properties = new Properties();
- properties.setProperty(FlowLineFeeder.FLOW_LINE_DROP_BOX_TEMPLATE, new File(
+ properties.setProperty(FlowLaneFeeder.FLOW_LANE_DROP_BOX_TEMPLATE, new File(
workingDirectory, DROP_BOX_PREFIX).getAbsolutePath()
+ "{0}");
- properties.setProperty(FlowLineFeeder.TRANSFER_PREFIX + AFFILIATION, transferDropBox.getAbsolutePath());
- flowLineFeeder = new FlowLineFeeder(properties, service);
+ properties.setProperty(FlowLaneFeeder.TRANSFER_PREFIX + AFFILIATION, transferDropBox.getAbsolutePath());
+ flowLaneFeeder = new FlowLaneFeeder(properties, service);
}
@AfterMethod
@@ -122,11 +123,11 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
{
try
{
- new FlowLineFeeder(new Properties(), service);
+ new FlowLaneFeeder(new Properties(), service);
fail("ConfigurationFailureException expected");
} catch (ConfigurationFailureException ex)
{
- assertEquals("Given key '" + FlowLineFeeder.FLOW_LINE_DROP_BOX_TEMPLATE
+ assertEquals("Given key '" + FlowLaneFeeder.FLOW_LANE_DROP_BOX_TEMPLATE
+ "' not found in properties '[]'", ex.getMessage());
}
@@ -138,13 +139,13 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
{
File flowCell = new File(workingDirectory, SAMPLE_CODE);
assertEquals(true, flowCell.mkdir());
- FileUtilities.writeToFile(new File(flowCell, "s_3.srf"), "hello flow line 3");
+ FileUtilities.writeToFile(new File(flowCell, "s_3.srf"), "hello flow lane 3");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
- prepareListFlowLines(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.<Sample>asList());
+ prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.<Sample>asList());
try
{
- flowLineFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
+ flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
fail("ConfigurationFailureException expected");
} catch (ConfigurationFailureException ex)
{
@@ -162,7 +163,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
try
{
- flowLineFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
+ flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
fail("UserFailureException expected");
} catch (UserFailureException ex)
{
@@ -174,7 +175,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
}
@Test
- public void testHappyCase()
+ public void testNotEnoughFlowLaneFiles()
{
File flowCell = new File(workingDirectory, SAMPLE_CODE);
assertEquals(true, flowCell.mkdir());
@@ -183,30 +184,61 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
FileUtilities.writeToFile(new File(logs, "basic.log"), "hello log");
File srfFolder = new File(flowCell, "SRF");
assertEquals(true, srfFolder.mkdir());
- File originalFlowLine1 = new File(srfFolder, "s_1.srf");
- FileUtilities.writeToFile(originalFlowLine1, "hello flow line 1");
- File originalFlowLine2 = new File(srfFolder, "2.srf");
- FileUtilities.writeToFile(originalFlowLine2, "hello flow line 2");
+ File originalFlowLane1 = new File(srfFolder, "s_1.srf");
+ FileUtilities.writeToFile(originalFlowLane1, "hello flow lane 1");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
- Sample fl1 = createFlowLineSample(1);
- Sample fl2 = createFlowLineSample(2);
- prepareListFlowLines(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.asList(fl1, fl2));
+ Sample fl1 = createFlowLaneSample(1);
+ Sample fl2 = createFlowLaneSample(2);
+ prepareListFlowLanes(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.asList(fl1, fl2));
- flowLineFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
+ try
+ {
+ flowLaneFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
+ fail("EnvironmentFailureException expected");
+ } catch (EnvironmentFailureException ex)
+ {
+ assertEquals("Only 1 flow lane files found instead of 2.", ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testHappyCase()
+ {
+ File flowCell = new File(workingDirectory, SAMPLE_CODE);
+ assertEquals(true, flowCell.mkdir());
+ File logs = new File(flowCell, "logs");
+ assertEquals(true, logs.mkdir());
+ FileUtilities.writeToFile(new File(logs, "basic.log"), "hello log");
+ File srfFolder = new File(flowCell, "SRF");
+ assertEquals(true, srfFolder.mkdir());
+ File originalFlowLane1 = new File(srfFolder, "s_1.srf");
+ FileUtilities.writeToFile(originalFlowLane1, "hello flow lane 1");
+ File originalFlowLane2 = new File(srfFolder, "2.srf");
+ FileUtilities.writeToFile(originalFlowLane2, "hello flow lane 2");
+ prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
- checkFlowLineDataSet(originalFlowLine1, "1");
- checkFlowLineDataSet(originalFlowLine2, "2");
+ 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";
assertEquals("G2_" + sampleName, transferedFiles[0].getName());
- File metaFile = getFile(transferedFiles[0], FlowLineFeeder.META_DATA_FILE_TYPE);
- assertEquals(sampleName + "_" + EXTERNAL_SAMPLE_NAME + FlowLineFeeder.META_DATA_FILE_TYPE,
+ File metaFile = getFile(transferedFiles[0], FlowLaneFeeder.META_DATA_FILE_TYPE);
+ assertEquals(sampleName + "_" + EXTERNAL_SAMPLE_NAME + FlowLaneFeeder.META_DATA_FILE_TYPE,
metaFile.getName());
- assertHardLinkOnSameFile(originalFlowLine2, getFile(transferedFiles[0], "2.srf"));
+ assertHardLinkOnSameFile(originalFlowLane2, getFile(transferedFiles[0], "2.srf"));
context.assertIsSatisfied();
}
@@ -232,7 +264,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
assertEquals(2, dropBox2.list().length);
assertEquals(1, transferDropBox.list().length);
- flowLineFeeder.undoLastOperation();
+ flowLaneFeeder.undoLastOperation();
assertEquals(0, dropBox1.list().length);
assertEquals(0, dropBox2.list().length);
@@ -250,7 +282,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
});
}
- private void prepareListFlowLines(final Sample flowCellSample, final List<Sample> flowLineSamples)
+ private void prepareListFlowLanes(final Sample flowCellSample, final List<Sample> flowLaneSamples)
{
context.checking(new Expectations()
{
@@ -275,8 +307,17 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
+ flowCellSample.getId());
}
}));
- will(returnValue(flowLineSamples));
- for (Sample sample : flowLineSamples)
+ will(returnValue(flowLaneSamples));
+ }
+ });
+ }
+
+ private void prepareGetProperties(final List<Sample> flowLaneSamples)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ for (Sample sample : flowLaneSamples)
{
SampleIdentifier identifier =
SampleIdentifierFactory.parse(sample.getIdentifier());
@@ -284,11 +325,12 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
if (sample.getSubCode().equals("2"))
{
GenericValueEntityProperty p1 =
- createProperty(FlowLineFeeder.AFFILIATION_KEY, AFFILIATION);
+ createProperty(FlowLaneFeeder.AFFILIATION_KEY, AFFILIATION);
GenericValueEntityProperty p2 =
- createProperty(FlowLineFeeder.EXTERNAL_SAMPLE_NAME_KEY,
+ createProperty(FlowLaneFeeder.EXTERNAL_SAMPLE_NAME_KEY,
EXTERNAL_SAMPLE_NAME);
- will(returnValue(new GenericValueEntityProperty[] {p1, p2}));
+ will(returnValue(new GenericValueEntityProperty[]
+ { p1, p2 }));
}
}
}
@@ -305,26 +347,26 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
}
});
}
-
- private void checkFlowLineDataSet(File originalFlowLine, String flowLineNumber)
+
+ private void checkFlowLaneDataSet(File originalFlowLane, String flowLaneNumber)
{
- File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLineNumber);
- String flowLineSampleCode =
+ File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLaneNumber);
+ String flowLaneSampleCode =
SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING
- + flowLineNumber;
+ + flowLaneNumber;
String fileName =
- "G" + flowLineNumber + FlowLineFeeder.DEFAULT_ENTITY_SEPARATOR + flowLineSampleCode;
+ "G" + flowLaneNumber + FlowLaneFeeder.DEFAULT_ENTITY_SEPARATOR + flowLaneSampleCode;
File ds = new File(dropBox, fileName);
assertEquals(true, ds.isDirectory());
- File flowLine = new File(ds, originalFlowLine.getName());
- assertEquals(true, flowLine.isFile());
- assertEquals(FileUtilities.loadToString(originalFlowLine), FileUtilities
- .loadToString(flowLine));
- assertHardLinkOnSameFile(originalFlowLine, flowLine);
+ File flowLane = new File(ds, originalFlowLane.getName());
+ assertEquals(true, flowLane.isFile());
+ assertEquals(FileUtilities.loadToString(originalFlowLane), FileUtilities
+ .loadToString(flowLane));
+ assertHardLinkOnSameFile(originalFlowLane, flowLane);
String metaDataFileName =
- flowLineSampleCode + (flowLineNumber.equals("2") ? "_" + EXTERNAL_SAMPLE_NAME : "")
- + FlowLineFeeder.META_DATA_FILE_TYPE;
+ flowLaneSampleCode + (flowLaneNumber.equals("2") ? "_" + EXTERNAL_SAMPLE_NAME : "")
+ + FlowLaneFeeder.META_DATA_FILE_TYPE;
assertEquals(true, new File(ds, metaDataFileName).exists());
assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists());
}
@@ -337,21 +379,21 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
assertEquals(4711000, file2.lastModified());
}
- private Sample createFlowLineSample(int flowLineNumber)
+ private Sample createFlowLaneSample(int flowLaneNumber)
{
Sample sample = new Sample();
sample.setCode(SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING
- + flowLineNumber);
+ + flowLaneNumber);
Group group = new Group();
- group.setCode("G" + flowLineNumber);
+ group.setCode("G" + flowLaneNumber);
sample.setGroup(group);
- sample.setSubCode(Integer.toString(flowLineNumber));
+ sample.setSubCode(Integer.toString(flowLaneNumber));
sample.setGeneratedFrom(EXAMPLE_FLOW_CELL_SAMPLE);
Person registrator = new Person();
registrator.setEmail("ab@c.de");
sample.setRegistrator(registrator);
sample.setIdentifier(SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING
- + flowLineNumber);
+ + flowLaneNumber);
return sample;
}
--
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