diff --git a/deep_sequencing_unit/.classpath b/deep_sequencing_unit/.classpath
index 1bdaf2704e297950b0150d5586117489a17d0f60..99c204da58b5c2982409fe3351ea360722baf353 100644
--- a/deep_sequencing_unit/.classpath
+++ b/deep_sequencing_unit/.classpath
@@ -12,5 +12,6 @@
<classpathentry kind="lib" path="/libraries/jmock/hamcrest/hamcrest-library.jar"/>
<classpathentry kind="lib" path="/libraries/jmock/objenesis/objenesis-1.0.jar"/>
<classpathentry kind="lib" path="/libraries/jmock/jmock.jar"/>
+ <classpathentry kind="lib" path="/libraries/log4j/log4j.jar" sourcepath="/libraries/log4j/src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
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 144306f2bb868ad3b2f26d20cac0840915e581ee..4b01c89a8268bb1b312a37b08a45498bb16ad3e4 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
@@ -19,10 +19,15 @@ package ch.ethz.bsse.cisd.dsu.dss;
import java.io.File;
import java.text.MessageFormat;
import java.util.ArrayList;
+import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import java.util.Properties;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import org.apache.log4j.Logger;
import ch.systemsx.cisd.common.Constants;
import ch.systemsx.cisd.common.TimingParameters;
@@ -33,6 +38,9 @@ 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.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.utilities.ExtendedProperties;
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;
@@ -41,6 +49,7 @@ import ch.systemsx.cisd.openbis.generic.client.web.client.exception.UserFailureE
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.PropertyType;
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;
@@ -53,15 +62,21 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
*/
class FlowLineFeeder implements IPostRegistrationDatasetHandler
{
+ static final String TRANSFER_PREFIX = "transfer.";
+ static final String AFFILIATION_KEY = "AFFILIATION";
static final String META_DATA_FILE_NAME = "meta-data.tsv";
static final String FLOW_LINE_DROP_BOX_TEMPLATE = "flow-line-drop-box-template";
static final String FILE_TYPE = ".srf";
+ private final static Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, FlowLineFeeder.class);
+
private final IEncapsulatedOpenBISService service;
private final MessageFormat flowLineDropBoxTemplate;
private final IImmutableCopier copier;
private final IFileOperations fileOperations;
- private final List<File> flowLineDataSets = new ArrayList<File>();
+ private final List<File> createdFiles = new ArrayList<File>();
+ private final Map<String, File> transferDropBoxes = new HashMap<String, File>();
FlowLineFeeder(Properties properties, IEncapsulatedOpenBISService service)
{
@@ -71,6 +86,21 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
FLOW_LINE_DROP_BOX_TEMPLATE));
copier = FastRecursiveHardLinkMaker.tryCreate(TimingParameters.getDefaultParameters());
fileOperations = FileOperations.getInstance();
+ Properties transferDropBoxMapping =
+ ExtendedProperties.getSubset(properties, TRANSFER_PREFIX, true);
+ Set<Entry<Object, Object>> entries = transferDropBoxMapping.entrySet();
+ for (Entry<Object, Object> entry : entries)
+ {
+ String affiliation = entry.getKey().toString();
+ String dropBoxPath = entry.getValue().toString();
+ File dropBox = new File(dropBoxPath);
+ if (dropBox.isDirectory() == false)
+ {
+ throw new EnvironmentFailureException("Transfer drop box for " + affiliation
+ + " doen't exist or isn't a folder: " + dropBox.getAbsolutePath());
+ }
+ transferDropBoxes.put(affiliation, dropBox);
+ }
}
public void handle(File originalData, DataSetInformation dataSetInformation)
@@ -90,24 +120,24 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
throw new EnvironmentFailureException("There is already a data set for flow line "
+ flowLine + ".");
}
- flowLineDataSets.add(flowLineDataSet);
+ createdFiles.add(flowLineDataSet);
boolean success = flowLineDataSet.mkdir();
if (success == false)
{
throw new EnvironmentFailureException("Couldn't create folder '"
+ flowLineDataSet.getAbsolutePath() + "'.");
}
- createMetaDataFile(flowLineDataSet, flowLineSampleMap, flowLine);
- success = copier.copyImmutably(file, flowLineDataSet, null);
- if (success == false)
- {
- throw new EnvironmentFailureException("Couldn't create a hard-link copy of '"
- + file.getAbsolutePath() + "' in folder '"
- + flowLineDataSet.getAbsolutePath() + "'.");
- }
+ createHartLink(file, flowLineDataSet);
+ createMetaDataFileAndHartLinkInTransferDropBox(flowLineDataSet, flowLineSampleMap, flowLine);
File markerFile = new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName);
- flowLineDataSets.add(markerFile);
+ createdFiles.add(markerFile);
FileUtilities.writeToFile(markerFile, "");
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("Flow line file '" + file
+ + "' successfully dropped into drop box '" + dropBox
+ + "' as '" + flowLineDataSet.getName() + "'.");
+ }
}
}
@@ -131,8 +161,8 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
return flowLineSampleMap;
}
- private void createMetaDataFile(File flowLineDataSet, Map<String, Sample> flowLineSampleMap,
- String flowLine)
+ private void createMetaDataFileAndHartLinkInTransferDropBox(File flowLineDataSet,
+ Map<String, Sample> flowLineSampleMap, String flowLine)
{
Sample flowLineSample = flowLineSampleMap.get(flowLine);
if (flowLineSample == null)
@@ -145,11 +175,28 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
addLine(builder, "Contact Person Email", flowLineSample.getRegistrator().getEmail());
SampleIdentifier identifier = SampleIdentifierFactory.parse(flowLineSample.getIdentifier());
IEntityProperty[] properties = service.getPropertiesOfTopSampleRegisteredFor(identifier);
+ File dropBox = null;
for (IEntityProperty property : properties)
{
- addLine(builder, property.getPropertyType().getLabel(), property.tryGetAsString());
+ PropertyType propertyType = property.getPropertyType();
+ String value = property.tryGetAsString();
+ addLine(builder, propertyType.getLabel(), value);
+ if (propertyType.getCode().equals(AFFILIATION_KEY))
+ {
+ dropBox = transferDropBoxes.get(value);
+ }
}
FileUtilities.writeToFile(new File(flowLineDataSet, META_DATA_FILE_NAME), builder.toString());
+ if (dropBox != null)
+ {
+ createHartLink(flowLineDataSet, dropBox);
+ createdFiles.add(new File(dropBox, flowLineDataSet.getName()));
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("Flow line data set '" + flowLineDataSet.getName()
+ + "' successfully transfered to drop box '" + dropBox + "'");
+ }
+ }
}
private void addLine(StringBuilder builder, String key, String value)
@@ -157,6 +204,18 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
builder.append(key).append('\t').append(value).append('\n');
}
+ private void createHartLink(File file, File folder)
+ {
+ boolean success;
+ success = copier.copyImmutably(file, folder, null);
+ if (success == false)
+ {
+ throw new EnvironmentFailureException("Couldn't create a hard-link copy of '"
+ + file.getAbsolutePath() + "' in folder '"
+ + folder.getAbsolutePath() + "'.");
+ }
+ }
+
private File createDropBoxFile(String flowLine)
{
File dropBox = new File(flowLineDropBoxTemplate.format(new Object[] {flowLine}));
@@ -201,7 +260,12 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
public void undoLastOperation()
{
- for (File file : flowLineDataSets)
+ if (operationLog.isInfoEnabled())
+ {
+ operationLog.info("Undo last operation by deleting following files: " + createdFiles);
+ }
+
+ for (File file : createdFiles)
{
if (file.exists())
{
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 b91f946efd50575487485cc63d4f22dc3ed45f2b..52bbe053e41a282565e42eba709d1c7a571b1310 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
@@ -17,6 +17,7 @@
package ch.ethz.bsse.cisd.dsu.dss;
import java.io.File;
+import java.io.FilenameFilter;
import java.io.IOException;
import java.util.Arrays;
import java.util.List;
@@ -34,12 +35,15 @@ 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.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.logging.LogInitializer;
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.GenericValueEntityProperty;
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.PropertyType;
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;
@@ -51,6 +55,8 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SampleIdentifierFa
*/
public class FlowLineFeederTest extends AbstractFileSystemTestCase
{
+ private static final String AFFILIATION = "fmi";
+ 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";
@@ -74,20 +80,30 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
private FlowLineFeeder flowLineFeeder;
private Mockery context;
private IEncapsulatedOpenBISService service;
+ private File dropBox1;
+ private File dropBox2;
+ private File transferDropBox;
@Override
@BeforeMethod
public void setUp() throws IOException
{
super.setUp();
+ LogInitializer.init();
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());
+ FileUtilities.deleteRecursively(workingDirectory);
+ dropBox1 = new File(workingDirectory, DROP_BOX_PREFIX + "1");
+ assertEquals(true, dropBox1.mkdirs());
+ dropBox2 = new File(workingDirectory, DROP_BOX_PREFIX + "2");
+ assertEquals(true, dropBox2.mkdirs());
+ 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(
workingDirectory, DROP_BOX_PREFIX).getAbsolutePath()
+ "{0}");
+ properties.setProperty(FlowLineFeeder.TRANSFER_PREFIX + AFFILIATION, transferDropBox.getAbsolutePath());
flowLineFeeder = new FlowLineFeeder(properties, service);
}
@@ -180,20 +196,42 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
checkFlowLineDataSet(originalFlowLine1, "1");
checkFlowLineDataSet(originalFlowLine2, "2");
+ File[] transferedFiles = transferDropBox.listFiles();
+ assertEquals(1, transferedFiles.length);
+ assertEquals("abc_2", transferedFiles[0].getName());
+ getFile(transferedFiles[0], FlowLineFeeder.META_DATA_FILE_NAME);
+ assertHardLinkOnSameFile(originalFlowLine2, getFile(transferedFiles[0], "2.srf"));
+
context.assertIsSatisfied();
}
+ private File getFile(File folder, final String fileName)
+ {
+ File[] files = folder.listFiles(new FilenameFilter()
+ {
+
+ public boolean accept(File dir, String name)
+ {
+ return fileName.equals(name);
+ }
+ });
+ assertEquals(1, files.length);
+ return files[0];
+ }
+
@Test
public void testUndoLastOperation()
{
testHappyCase();
- assertEquals(2, new File(workingDirectory, DROP_BOX_PREFIX + "1").list().length);
- assertEquals(2, new File(workingDirectory, DROP_BOX_PREFIX + "2").list().length);
+ assertEquals(2, dropBox1.list().length);
+ assertEquals(2, dropBox2.list().length);
+ assertEquals(1, transferDropBox.list().length);
flowLineFeeder.undoLastOperation();
- assertEquals(0, new File(workingDirectory, DROP_BOX_PREFIX + "1").list().length);
- assertEquals(0, new File(workingDirectory, DROP_BOX_PREFIX + "2").list().length);
+ assertEquals(0, dropBox1.list().length);
+ assertEquals(0, dropBox2.list().length);
+ assertEquals(0, transferDropBox.list().length);
}
private void prepareLoadFlowCellSample(final Sample flowCellSample)
@@ -238,6 +276,16 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
SampleIdentifier identifier =
SampleIdentifierFactory.parse(sample.getIdentifier());
one(service).getPropertiesOfTopSampleRegisteredFor(identifier);
+ if (sample.getSubCode().equals("2"))
+ {
+ GenericValueEntityProperty p = new GenericValueEntityProperty();
+ p.setValue(AFFILIATION);
+ PropertyType propertyType = new PropertyType();
+ propertyType.setCode(FlowLineFeeder.AFFILIATION_KEY);
+ propertyType.setLabel(FlowLineFeeder.AFFILIATION_KEY.toLowerCase());
+ p.setPropertyType(propertyType);
+ will(returnValue(new GenericValueEntityProperty[] {p}));
+ }
}
}
});
@@ -254,13 +302,18 @@ public class FlowLineFeederTest extends AbstractFileSystemTestCase
assertEquals(true, flowLine.isFile());
assertEquals(FileUtilities.loadToString(originalFlowLine), FileUtilities
.loadToString(flowLine));
- // check hard-link copy by changing last-modified date of one file should change
- // last-modified date of the other file.
- originalFlowLine.setLastModified(4711000);
- assertEquals(4711000, flowLine.lastModified());
+ assertHardLinkOnSameFile(originalFlowLine, flowLine);
assertEquals(true, new File(ds, FlowLineFeeder.META_DATA_FILE_NAME).exists());
assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists());
}
+
+ private void assertHardLinkOnSameFile(File file1, File file2)
+ {
+ // check hard-link copy by changing last-modified date of one file should change
+ // last-modified date of the other file.
+ file1.setLastModified(4711000);
+ assertEquals(4711000, file2.lastModified());
+ }
private Sample createFlowLineSample(int flowLineNumber)
{