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Commit 0b0cb3c4 authored by felmer's avatar felmer
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LMS-1218 Few changes: Metafile name contains flow line sample code and... 

LMS-1218 Few changes: Metafile name contains flow line sample code and property EXTERNAL_SAMPLE_NAME, Flow Line Data Set name contains group code and sample code with ':' instead of '_'. Flow line ETL thread examples added to service.properties

SVN: 12906
parent 9fd51171
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deep_sequencing_unit/dist/etc/service.properties
+ 23
− 1
View file @ 0b0cb3c4
...@@ -86,7 +86,7 @@ data-set-file-name-entity-separator = _ ...@@ -86,7 +86,7 @@ data-set-file-name-entity-separator = _
# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name. # Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor' # E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
inputs = flow-cell inputs = flow-cell, fl1, fl2
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# 'flow-cell' thread configuration # 'flow-cell' thread configuration
...@@ -126,3 +126,25 @@ flow-cell.storage-processor = ch.ethz.bsse.cisd.dsu.dss.StorageProcessor ...@@ -126,3 +126,25 @@ flow-cell.storage-processor = ch.ethz.bsse.cisd.dsu.dss.StorageProcessor
flow-cell.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor flow-cell.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
# Template of flow-line drop boxes. {0} is the place holder for flow line number # Template of flow-line drop boxes. {0} is the place holder for flow line number
flow-cell.storage-processor.flow-line-drop-box-template = data/drop-box-{0} flow-cell.storage-processor.flow-line-drop-box-template = data/drop-box-{0}
flow-cell.storage-processor.transfer.BSSE = data/drop-box-bsse
# -------- Flow Line 1 --------------------------------------
fl1.incoming-dir = data/drop-box-1
fl1.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
fl1.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
fl1.data-set-info-extractor.index-of-group-code = 0
fl1.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
fl1.type-extractor.file-format-type = PROPRIETARY
fl1.type-extractor.data-set-type = FLOW_LINE
fl1.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
# -------- Flow Line 2 --------------------------------------
fl2.incoming-dir = data/drop-box-2
fl2.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
fl2.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
fl2.data-set-info-extractor.index-of-group-code = 0
fl2.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
fl2.type-extractor.file-format-type = PROPRIETARY
fl2.type-extractor.data-set-type = FLOW_LINE
fl2.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
deep_sequencing_unit/etc/service.properties
+ 25
− 2
View file @ 0b0cb3c4
...@@ -86,7 +86,7 @@ data-set-file-name-entity-separator = _ ...@@ -86,7 +86,7 @@ data-set-file-name-entity-separator = _
# Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name. # Comma separated names of processing threads. Each thread should have configuration properties prefixed with its name.
# E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor' # E.g. 'code-extractor' property for the thread 'my-etl' should be specified as 'my-etl.code-extractor'
inputs = flow-cell inputs = flow-cell, fl1, fl2
# --------------------------------------------------------------------------- # ---------------------------------------------------------------------------
# 'flow-cell' thread configuration # 'flow-cell' thread configuration
...@@ -118,10 +118,33 @@ flow-cell.data-set-info-extractor.group-code = TEST ...@@ -118,10 +118,33 @@ flow-cell.data-set-info-extractor.group-code = TEST
flow-cell.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor flow-cell.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
flow-cell.type-extractor.file-format-type = PROPRIETARY flow-cell.type-extractor.file-format-type = PROPRIETARY
flow-cell.type-extractor.locator-type = RELATIVE_LOCATION flow-cell.type-extractor.locator-type = RELATIVE_LOCATION
flow-cell.type-extractor.data-set-type = FLOW_LINE flow-cell.type-extractor.data-set-type = FLOW_CELL
flow-cell.type-extractor.is-measured = true flow-cell.type-extractor.is-measured = true
# The storage processor (IStorageProcessor implementation) # The storage processor (IStorageProcessor implementation)
flow-cell.storage-processor = ch.ethz.bsse.cisd.dsu.dss.StorageProcessor flow-cell.storage-processor = ch.ethz.bsse.cisd.dsu.dss.StorageProcessor
flow-cell.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor flow-cell.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
flow-cell.storage-processor.flow-line-drop-box-template = targets/playground/drop-box-{0} flow-cell.storage-processor.flow-line-drop-box-template = targets/playground/drop-box-{0}
flow-cell.storage-processor.entity-separator = ${data-set-file-name-entity-separator}
flow-cell.storage-processor.transfer.FMI = targets/playground/drop-box-fmi
# -------- Flow Line 1 --------------------------------------
fl1.incoming-dir = targets/playground/drop-box-1
fl1.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
fl1.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
fl1.data-set-info-extractor.index-of-group-code = 0
fl1.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
fl1.type-extractor.file-format-type = PROPRIETARY
fl1.type-extractor.data-set-type = FLOW_LINE
fl1.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
# -------- Flow Line 2 --------------------------------------
fl2.incoming-dir = targets/playground/drop-box-2
fl2.data-set-info-extractor = ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor
fl2.data-set-info-extractor.entity-separator = ${data-set-file-name-entity-separator}
fl2.data-set-info-extractor.index-of-group-code = 0
fl2.type-extractor = ch.systemsx.cisd.etlserver.SimpleTypeExtractor
fl2.type-extractor.file-format-type = PROPRIETARY
fl2.type-extractor.data-set-type = FLOW_LINE
fl2.storage-processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor
deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeeder.java
+ 23
− 7
View file @ 0b0cb3c4
...@@ -62,10 +62,13 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa ...@@ -62,10 +62,13 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
*/ */
class FlowLineFeeder implements IPostRegistrationDatasetHandler class FlowLineFeeder implements IPostRegistrationDatasetHandler
{ {
static final String META_DATA_FILE_TYPE = ".tsv";
static final String TRANSFER_PREFIX = "transfer."; static final String TRANSFER_PREFIX = "transfer.";
static final String AFFILIATION_KEY = "AFFILIATION"; static final String AFFILIATION_KEY = "AFFILIATION";
static final String META_DATA_FILE_NAME = "meta-data.tsv"; 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_LINE_DROP_BOX_TEMPLATE = "flow-line-drop-box-template";
static final String ENTITY_SEPARATOR_KEY = "entity-separator";
static final String DEFAULT_ENTITY_SEPARATOR = "_";
static final String FILE_TYPE = ".srf"; static final String FILE_TYPE = ".srf";
private final static Logger operationLog = private final static Logger operationLog =
...@@ -73,6 +76,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler ...@@ -73,6 +76,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
private final IEncapsulatedOpenBISService service; private final IEncapsulatedOpenBISService service;
private final MessageFormat flowLineDropBoxTemplate; private final MessageFormat flowLineDropBoxTemplate;
private final String entitySepaparator;
private final IImmutableCopier copier; private final IImmutableCopier copier;
private final IFileOperations fileOperations; private final IFileOperations fileOperations;
private final List<File> createdFiles = new ArrayList<File>(); private final List<File> createdFiles = new ArrayList<File>();
...@@ -84,6 +88,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler ...@@ -84,6 +88,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
flowLineDropBoxTemplate = flowLineDropBoxTemplate =
new MessageFormat(PropertyUtils.getMandatoryProperty(properties, new MessageFormat(PropertyUtils.getMandatoryProperty(properties,
FLOW_LINE_DROP_BOX_TEMPLATE)); FLOW_LINE_DROP_BOX_TEMPLATE));
entitySepaparator = properties.getProperty(ENTITY_SEPARATOR_KEY, DEFAULT_ENTITY_SEPARATOR);
copier = FastRecursiveHardLinkMaker.tryCreate(TimingParameters.getDefaultParameters()); copier = FastRecursiveHardLinkMaker.tryCreate(TimingParameters.getDefaultParameters());
fileOperations = FileOperations.getInstance(); fileOperations = FileOperations.getInstance();
Properties transferDropBoxMapping = Properties transferDropBoxMapping =
...@@ -112,8 +117,11 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler ...@@ -112,8 +117,11 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
for (File file : files) for (File file : files)
{ {
String flowLine = extractFlowLine(file); String flowLine = extractFlowLine(file);
Sample flowLineSample = flowLineSampleMap.get(flowLine);
File dropBox = createDropBoxFile(flowLine); File dropBox = createDropBoxFile(flowLine);
String fileName = flowcellID + "_" + flowLine; String fileName =
flowLineSample.getGroup().getCode() + entitySepaparator + flowcellID
+ SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + flowLine;
File flowLineDataSet = new File(dropBox, fileName); File flowLineDataSet = new File(dropBox, fileName);
if (flowLineDataSet.exists()) if (flowLineDataSet.exists())
{ {
...@@ -128,7 +136,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler ...@@ -128,7 +136,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
+ flowLineDataSet.getAbsolutePath() + "'."); + flowLineDataSet.getAbsolutePath() + "'.");
} }
createHartLink(file, flowLineDataSet); createHartLink(file, flowLineDataSet);
createMetaDataFileAndHartLinkInTransferDropBox(flowLineDataSet, flowLineSampleMap, flowLine); createMetaDataFileAndHartLinkInTransferDropBox(flowLineDataSet, flowLineSample, flowLine);
File markerFile = new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName); File markerFile = new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName);
createdFiles.add(markerFile); createdFiles.add(markerFile);
FileUtilities.writeToFile(markerFile, ""); FileUtilities.writeToFile(markerFile, "");
...@@ -162,9 +170,8 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler ...@@ -162,9 +170,8 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
} }
private void createMetaDataFileAndHartLinkInTransferDropBox(File flowLineDataSet, private void createMetaDataFileAndHartLinkInTransferDropBox(File flowLineDataSet,
Map<String, Sample> flowLineSampleMap, String flowLine) Sample flowLineSample, String flowLine)
{ {
Sample flowLineSample = flowLineSampleMap.get(flowLine);
if (flowLineSample == null) if (flowLineSample == null)
{ {
throw new UserFailureException("No flow line sample for flow line " + flowLine + " exists"); throw new UserFailureException("No flow line sample for flow line " + flowLine + " exists");
...@@ -176,17 +183,26 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler ...@@ -176,17 +183,26 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
SampleIdentifier identifier = SampleIdentifierFactory.parse(flowLineSample.getIdentifier()); SampleIdentifier identifier = SampleIdentifierFactory.parse(flowLineSample.getIdentifier());
IEntityProperty[] properties = service.getPropertiesOfTopSampleRegisteredFor(identifier); IEntityProperty[] properties = service.getPropertiesOfTopSampleRegisteredFor(identifier);
File dropBox = null; File dropBox = null;
String externalSampleName = null;
for (IEntityProperty property : properties) for (IEntityProperty property : properties)
{ {
PropertyType propertyType = property.getPropertyType(); PropertyType propertyType = property.getPropertyType();
String value = property.tryGetAsString(); String value = property.tryGetAsString();
addLine(builder, propertyType.getLabel(), value); addLine(builder, propertyType.getLabel(), value);
if (propertyType.getCode().equals(AFFILIATION_KEY)) String code = propertyType.getCode();
if (code.equals(AFFILIATION_KEY))
{ {
dropBox = transferDropBoxes.get(value); dropBox = transferDropBoxes.get(value);
} }
if (code.equals(EXTERNAL_SAMPLE_NAME_KEY))
{
externalSampleName = value;
}
} }
FileUtilities.writeToFile(new File(flowLineDataSet, META_DATA_FILE_NAME), builder.toString()); String metaFileName =
flowLineSample.getCode()
+ (externalSampleName == null ? "" : "_" + externalSampleName) + META_DATA_FILE_TYPE;
FileUtilities.writeToFile(new File(flowLineDataSet, metaFileName), builder.toString());
if (dropBox != null) if (dropBox != null)
{ {
createHartLink(flowLineDataSet, dropBox); createHartLink(flowLineDataSet, dropBox);
......
deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
+ 44
− 18
View file @ 0b0cb3c4
...@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService; ...@@ -41,6 +41,7 @@ import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation; import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException; import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureException;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericValueEntityProperty; import ch.systemsx.cisd.openbis.generic.shared.basic.dto.GenericValueEntityProperty;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Group;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria; import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person; import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType; import ch.systemsx.cisd.openbis.generic.shared.basic.dto.PropertyType;
...@@ -56,6 +57,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa ...@@ -56,6 +57,7 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
public class FlowLineFeederTest extends AbstractFileSystemTestCase public class FlowLineFeederTest extends AbstractFileSystemTestCase
{ {
private static final String AFFILIATION = "fmi"; 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 String TRANSFER_DROP_BOX = "transfer-drop-box";
private static final Sample EXAMPLE_FLOW_CELL_SAMPLE = createFlowCellSample(); private static final Sample EXAMPLE_FLOW_CELL_SAMPLE = createFlowCellSample();
private static final DataSetInformation EXAMPLE_DATA_SET_INFO = createDataSetInfo(); private static final DataSetInformation EXAMPLE_DATA_SET_INFO = createDataSetInfo();
...@@ -134,7 +136,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase ...@@ -134,7 +136,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
@Test @Test
void testMissingDropBox() void testMissingDropBox()
{ {
File flowCell = new File(workingDirectory, "abc"); File flowCell = new File(workingDirectory, SAMPLE_CODE);
assertEquals(true, flowCell.mkdir()); 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 line 3");
prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE); prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
...@@ -155,7 +157,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase ...@@ -155,7 +157,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
@Test @Test
public void testUnkownFlowCell() public void testUnkownFlowCell()
{ {
File flowCell = new File(workingDirectory, "abc"); File flowCell = new File(workingDirectory, SAMPLE_CODE);
prepareLoadFlowCellSample(null); prepareLoadFlowCellSample(null);
try try
...@@ -174,7 +176,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase ...@@ -174,7 +176,7 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
@Test @Test
public void testHappyCase() public void testHappyCase()
{ {
File flowCell = new File(workingDirectory, "abc"); File flowCell = new File(workingDirectory, SAMPLE_CODE);
assertEquals(true, flowCell.mkdir()); assertEquals(true, flowCell.mkdir());
File logs = new File(flowCell, "logs"); File logs = new File(flowCell, "logs");
assertEquals(true, logs.mkdir()); assertEquals(true, logs.mkdir());
...@@ -198,21 +200,24 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase ...@@ -198,21 +200,24 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
File[] transferedFiles = transferDropBox.listFiles(); File[] transferedFiles = transferDropBox.listFiles();
assertEquals(1, transferedFiles.length); assertEquals(1, transferedFiles.length);
assertEquals("abc_2", transferedFiles[0].getName()); String sampleName =
getFile(transferedFiles[0], FlowLineFeeder.META_DATA_FILE_NAME); 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,
metaFile.getName());
assertHardLinkOnSameFile(originalFlowLine2, getFile(transferedFiles[0], "2.srf")); assertHardLinkOnSameFile(originalFlowLine2, getFile(transferedFiles[0], "2.srf"));
context.assertIsSatisfied(); context.assertIsSatisfied();
} }
private File getFile(File folder, final String fileName) private File getFile(File folder, final String fileNameExtension)
{ {
File[] files = folder.listFiles(new FilenameFilter() File[] files = folder.listFiles(new FilenameFilter()
{ {
public boolean accept(File dir, String name) public boolean accept(File dir, String name)
{ {
return fileName.equals(name); return name.endsWith(fileNameExtension);
} }
}); });
assertEquals(1, files.length); assertEquals(1, files.length);
...@@ -278,23 +283,37 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase ...@@ -278,23 +283,37 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
one(service).getPropertiesOfTopSampleRegisteredFor(identifier); one(service).getPropertiesOfTopSampleRegisteredFor(identifier);
if (sample.getSubCode().equals("2")) if (sample.getSubCode().equals("2"))
{ {
GenericValueEntityProperty p = new GenericValueEntityProperty(); GenericValueEntityProperty p1 =
p.setValue(AFFILIATION); createProperty(FlowLineFeeder.AFFILIATION_KEY, AFFILIATION);
PropertyType propertyType = new PropertyType(); GenericValueEntityProperty p2 =
propertyType.setCode(FlowLineFeeder.AFFILIATION_KEY); createProperty(FlowLineFeeder.EXTERNAL_SAMPLE_NAME_KEY,
propertyType.setLabel(FlowLineFeeder.AFFILIATION_KEY.toLowerCase()); EXTERNAL_SAMPLE_NAME);
p.setPropertyType(propertyType); will(returnValue(new GenericValueEntityProperty[] {p1, p2}));
will(returnValue(new GenericValueEntityProperty[] {p}));
} }
} }
} }
private GenericValueEntityProperty createProperty(String key, String value)
{
GenericValueEntityProperty p = new GenericValueEntityProperty();
p.setValue(value);
PropertyType propertyType = new PropertyType();
propertyType.setCode(key);
propertyType.setLabel(key.toLowerCase());
p.setPropertyType(propertyType);
return p;
}
}); });
} }
private void checkFlowLineDataSet(File originalFlowLine, String flowLineNumber) private void checkFlowLineDataSet(File originalFlowLine, String flowLineNumber)
{ {
File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLineNumber); File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLineNumber);
String fileName = "abc_" + flowLineNumber; String flowLineSampleCode =
SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING
+ flowLineNumber;
String fileName =
"G" + flowLineNumber + FlowLineFeeder.DEFAULT_ENTITY_SEPARATOR + flowLineSampleCode;
File ds = new File(dropBox, fileName); File ds = new File(dropBox, fileName);
assertEquals(true, ds.isDirectory()); assertEquals(true, ds.isDirectory());
...@@ -303,7 +322,10 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase ...@@ -303,7 +322,10 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
assertEquals(FileUtilities.loadToString(originalFlowLine), FileUtilities assertEquals(FileUtilities.loadToString(originalFlowLine), FileUtilities
.loadToString(flowLine)); .loadToString(flowLine));
assertHardLinkOnSameFile(originalFlowLine, flowLine); assertHardLinkOnSameFile(originalFlowLine, flowLine);
assertEquals(true, new File(ds, FlowLineFeeder.META_DATA_FILE_NAME).exists()); String metaDataFileName =
flowLineSampleCode + (flowLineNumber.equals("2") ? "_" + EXTERNAL_SAMPLE_NAME : "")
+ FlowLineFeeder.META_DATA_FILE_TYPE;
assertEquals(true, new File(ds, metaDataFileName).exists());
assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists()); assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists());
} }
...@@ -318,7 +340,11 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase ...@@ -318,7 +340,11 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
private Sample createFlowLineSample(int flowLineNumber) private Sample createFlowLineSample(int flowLineNumber)
{ {
Sample sample = new Sample(); Sample sample = new Sample();
sample.setCode(SAMPLE_CODE); sample.setCode(SAMPLE_CODE + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING
+ flowLineNumber);
Group group = new Group();
group.setCode("G" + flowLineNumber);
sample.setGroup(group);
sample.setSubCode(Integer.toString(flowLineNumber)); sample.setSubCode(Integer.toString(flowLineNumber));
sample.setGeneratedFrom(EXAMPLE_FLOW_CELL_SAMPLE); sample.setGeneratedFrom(EXAMPLE_FLOW_CELL_SAMPLE);
Person registrator = new Person(); Person registrator = new Person();
......
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