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/FlowLineFeeder.java
index 59dc4282012d00e4f234f352ecda6f726e7cee7e..b72a5910cb88044627a5a3238a38fe98583cd841 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/FlowLineFeeder.java
@@ -19,7 +19,9 @@ package ch.ethz.bsse.cisd.dsu.dss;
import java.io.File;
import java.text.MessageFormat;
import java.util.ArrayList;
+import java.util.LinkedHashMap;
import java.util.List;
+import java.util.Map;
import java.util.Properties;
import ch.systemsx.cisd.common.TimingParameters;
@@ -27,11 +29,20 @@ import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.filesystem.FastRecursiveHardLinkMaker;
import ch.systemsx.cisd.common.filesystem.FileOperations;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.filesystem.IFileOperations;
import ch.systemsx.cisd.common.filesystem.IImmutableCopier;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.IPostRegistrationDatasetHandler;
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.shared.basic.TechId;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IEntityProperty;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+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
@@ -44,13 +55,15 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
static final String FLOW_LINE_DROP_BOX_TEMPLATE = "flow-line-drop-box-template";
static final String FILE_TYPE = ".srf";
+ private final IEncapsulatedOpenBISService service;
private final MessageFormat flowLineDropBoxTemplate;
private final IImmutableCopier copier;
private final IFileOperations fileOperations;
private final List<File> flowLineDataSets = new ArrayList<File>();
- FlowLineFeeder(Properties properties)
+ FlowLineFeeder(Properties properties, IEncapsulatedOpenBISService service)
{
+ this.service = service;
flowLineDropBoxTemplate =
new MessageFormat(PropertyUtils.getMandatoryProperty(properties,
FLOW_LINE_DROP_BOX_TEMPLATE));
@@ -60,6 +73,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
public void handle(File originalData, DataSetInformation dataSetInformation)
{
+ Map<String, Sample> flowLineSampleMap = createFlowLineSampleMap(dataSetInformation);
String flowcellID = originalData.getName();
List<File> files = new ArrayList<File>();
findFiles(originalData, files);
@@ -68,6 +82,11 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
String flowLine = extractFlowLine(file);
File dropBox = createDropBoxFile(flowLine);
File flowLineDataSet = new File(dropBox, flowcellID + "_" + flowLine);
+ if (flowLineDataSet.exists())
+ {
+ throw new EnvironmentFailureException("There is already a data set for flow line "
+ + flowLine + ".");
+ }
flowLineDataSets.add(flowLineDataSet);
boolean success = flowLineDataSet.mkdir();
if (success == false)
@@ -75,6 +94,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
throw new EnvironmentFailureException("Couldn't create folder '"
+ flowLineDataSet.getAbsolutePath() + "'.");
}
+ createMetaDataFile(flowLineDataSet, flowLineSampleMap, flowLine);
success = copier.copyImmutably(file, flowLineDataSet, null);
if (success == false)
{
@@ -86,6 +106,51 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
}
+ private Map<String, Sample> createFlowLineSampleMap(DataSetInformation dataSetInformation)
+ {
+ SampleIdentifier sampleIdentifier = dataSetInformation.getSampleIdentifier();
+ Sample flowCell = service.tryGetSampleWithExperiment(sampleIdentifier);
+ if (flowCell == null)
+ {
+ throw new UserFailureException("Unkown flow cell sample: " + sampleIdentifier);
+ }
+ 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)
+ {
+ flowLineSampleMap.put(flowLineSample.getSubCode(), flowLineSample);
+ }
+ return flowLineSampleMap;
+ }
+
+ private void createMetaDataFile(File flowLineDataSet, Map<String, Sample> flowLineSampleMap,
+ String flowLine)
+ {
+ Sample flowLineSample = flowLineSampleMap.get(flowLine);
+ if (flowLineSample == null)
+ {
+ throw new UserFailureException("No flow line sample for flow line " + flowLine + " 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());
+ IEntityProperty[] properties = service.getPropertiesOfTopSampleRegisteredFor(identifier);
+ for (IEntityProperty property : properties)
+ {
+ addLine(builder, property.getPropertyType().getLabel(), property.tryGetAsString());
+ }
+ FileUtilities.writeToFile(new File(flowLineDataSet, "meta-data.tsv"), builder.toString());
+ }
+
+ private void addLine(StringBuilder builder, String key, String value)
+ {
+ builder.append(key).append('\t').append(value).append('\n');
+ }
+
private File createDropBoxFile(String flowLine)
{
File dropBox = new File(flowLineDropBoxTemplate.format(new Object[] {flowLine}));
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 0d9d4efbfb2c0e9d64350080d710ec27b1da9175..d220b5a0934bf5d47b66a2d2c5a7cc908f22eb80 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
@@ -19,6 +19,7 @@ package ch.ethz.bsse.cisd.dsu.dss;
import java.util.Properties;
import ch.systemsx.cisd.etlserver.DelegatingStorageProcessorWithDropbox;
+import ch.systemsx.cisd.openbis.dss.generic.shared.ServiceProvider;
/**
* Storage processor which feeds flow-line drop boxes. Needs the property
@@ -31,7 +32,7 @@ public class StorageProcessor extends DelegatingStorageProcessorWithDropbox
{
public StorageProcessor(Properties properties)
{
- super(properties, new FlowLineFeeder(properties));
+ super(properties, new FlowLineFeeder(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/FlowLineFeederTest.java
index 1c728db677aeea052ce4d920b7cf2b4020e6ed59..460fb5d30da19dd04052f9716706bed90c6062bd 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/FlowLineFeederTest.java
@@ -18,8 +18,15 @@ package ch.ethz.bsse.cisd.dsu.dss;
import java.io.File;
import java.io.IOException;
+import java.util.Arrays;
+import java.util.List;
import java.util.Properties;
+import org.hamcrest.BaseMatcher;
+import org.hamcrest.Description;
+import org.jmock.Expectations;
+import org.jmock.Mockery;
+import org.testng.annotations.AfterMethod;
import org.testng.annotations.BeforeMethod;
import org.testng.annotations.Test;
@@ -27,6 +34,14 @@ import ch.systemsx.cisd.base.tests.AbstractFileSystemTestCase;
import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.common.test.AssertionUtil;
+import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+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.shared.basic.dto.ListSampleCriteria;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Sample;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifier;
+import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFactory;
/**
*
@@ -35,21 +50,52 @@ import ch.systemsx.cisd.common.test.AssertionUtil;
*/
public class FlowLineFeederTest extends AbstractFileSystemTestCase
{
+ 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();
+ sample.setId(42L);
+ sample.setCode(SAMPLE_CODE);
+ return sample;
+ }
+
private FlowLineFeeder flowLineFeeder;
+ private Mockery context;
+ private IEncapsulatedOpenBISService service;
@Override
@BeforeMethod
public void setUp() throws IOException
{
super.setUp();
+ context = new Mockery();
+ service = context.mock(IEncapsulatedOpenBISService.class);
assertEquals(true, new File(workingDirectory, DROP_BOX_PREFIX + "1").mkdirs());
assertEquals(true, new File(workingDirectory, DROP_BOX_PREFIX + "2").mkdirs());
Properties properties = new Properties();
properties.setProperty(FlowLineFeeder.FLOW_LINE_DROP_BOX_TEMPLATE, new File(
workingDirectory, DROP_BOX_PREFIX).getAbsolutePath()
+ "{0}");
- flowLineFeeder = new FlowLineFeeder(properties);
+ flowLineFeeder = new FlowLineFeeder(properties, service);
+ }
+
+ @AfterMethod
+ public void tearDown()
+ {
+ // To following line of code should also be called at the end of each test method.
+ // Otherwise one does not known which test failed.
+ context.assertIsSatisfied();
}
@Test
@@ -57,13 +103,15 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
{
try
{
- new FlowLineFeeder(new Properties());
+ new FlowLineFeeder(new Properties(), service);
fail("ConfigurationFailureException expected");
} catch (ConfigurationFailureException ex)
{
assertEquals("Given key '" + FlowLineFeeder.FLOW_LINE_DROP_BOX_TEMPLATE
+ "' not found in properties '[]'", ex.getMessage());
}
+
+ context.assertIsSatisfied();
}
@Test
@@ -72,15 +120,38 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
File flowCell = new File(workingDirectory, "abc");
assertEquals(true, flowCell.mkdir());
FileUtilities.writeToFile(new File(flowCell, "s_3.srf"), "hello flow line 3");
+ prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
+ prepareListFlowLines(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.<Sample>asList());
try
{
- flowLineFeeder.handle(flowCell, null);
+ flowLineFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
fail("ConfigurationFailureException expected");
} catch (ConfigurationFailureException ex)
{
AssertionUtil.assertContains(DROP_BOX_PREFIX + "3", ex.getMessage());
}
+
+ context.assertIsSatisfied();
+ }
+
+ @Test
+ public void testUnkownFlowCell()
+ {
+ File flowCell = new File(workingDirectory, "abc");
+ prepareLoadFlowCellSample(null);
+
+ try
+ {
+ flowLineFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
+ fail("UserFailureException expected");
+ } catch (UserFailureException ex)
+ {
+ assertEquals("Unkown flow cell sample: " + EXAMPLE_DATA_SET_INFO.getSampleIdentifier(),
+ ex.getMessage());
+ }
+
+ context.assertIsSatisfied();
}
@Test
@@ -97,11 +168,18 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
FileUtilities.writeToFile(originalFlowLine1, "hello flow line 1");
File originalFlowLine2 = new File(srfFolder, "2.srf");
FileUtilities.writeToFile(originalFlowLine2, "hello flow line 2");
+ prepareLoadFlowCellSample(EXAMPLE_FLOW_CELL_SAMPLE);
+
+ Sample fl1 = createFlowLineSample(1);
+ Sample fl2 = createFlowLineSample(2);
+ prepareListFlowLines(EXAMPLE_FLOW_CELL_SAMPLE, Arrays.asList(fl1, fl2));
- flowLineFeeder.handle(flowCell, null);
+ flowLineFeeder.handle(flowCell, EXAMPLE_DATA_SET_INFO);
checkFlowLineDataSet(originalFlowLine1, "1");
checkFlowLineDataSet(originalFlowLine2, "2");
+
+ context.assertIsSatisfied();
}
@Test
@@ -116,6 +194,53 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
assertEquals(0, new File(workingDirectory, DROP_BOX_PREFIX + "1").list().length);
assertEquals(0, new File(workingDirectory, DROP_BOX_PREFIX + "2").list().length);
}
+
+ private void prepareLoadFlowCellSample(final Sample flowCellSample)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).tryGetSampleWithExperiment(EXAMPLE_DATA_SET_INFO.getSampleIdentifier());
+ will(returnValue(flowCellSample));
+ }
+ });
+ }
+
+ private void prepareListFlowLines(final Sample flowCellSample, final List<Sample> flowLineSamples)
+ {
+ context.checking(new Expectations()
+ {
+ {
+ one(service).listSamples(with(new BaseMatcher<ListSampleCriteria>()
+ {
+
+ public boolean matches(Object item)
+ {
+ if (item instanceof ListSampleCriteria)
+ {
+ ListSampleCriteria criteria = (ListSampleCriteria) item;
+ return criteria.getContainerSampleId().getId().equals(
+ flowCellSample.getId());
+ }
+ return false;
+ }
+
+ public void describeTo(Description description)
+ {
+ description.appendText("Flow cell with ID "
+ + flowCellSample.getId());
+ }
+ }));
+ will(returnValue(flowLineSamples));
+ for (Sample sample : flowLineSamples)
+ {
+ SampleIdentifier identifier =
+ SampleIdentifierFactory.parse(sample.getIdentifier());
+ one(service).getPropertiesOfTopSampleRegisteredFor(identifier);
+ }
+ }
+ });
+ }
private void checkFlowLineDataSet(File originalFlowLine, String flowLineNumber)
{
@@ -132,4 +257,19 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
originalFlowLine.setLastModified(4711000);
assertEquals(4711000, flowLine.lastModified());
}
+
+ private Sample createFlowLineSample(int flowLineNumber)
+ {
+ Sample sample = new Sample();
+ sample.setCode(SAMPLE_CODE);
+ sample.setSubCode(Integer.toString(flowLineNumber));
+ 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);
+ return sample;
+ }
+
}