diff --git a/deep_sequencing_unit/.classpath b/deep_sequencing_unit/.classpath
index 417fb1931958ed5f1692dab880073df47f1735a2..238c07c192773c1b5d8f0336c43075d687d8de07 100644
--- a/deep_sequencing_unit/.classpath
+++ b/deep_sequencing_unit/.classpath
@@ -6,5 +6,7 @@
<classpathentry combineaccessrules="false" kind="src" path="/datastore_server"/>
<classpathentry combineaccessrules="false" kind="src" path="/common"/>
<classpathentry kind="lib" path="/libraries/testng/testng-jdk15.jar" sourcepath="/libraries/testng/src.zip"/>
+ <classpathentry kind="lib" path="/libraries/cisd-base/cisd-base-test.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
+ <classpathentry kind="lib" path="/libraries/cisd-base/cisd-base.jar" sourcepath="/libraries/cisd-base/cisd-base-src.zip"/>
<classpathentry kind="output" path="targets/classes"/>
</classpath>
diff --git a/deep_sequencing_unit/dist/etc/service.properties b/deep_sequencing_unit/dist/etc/service.properties
index 6210f2c083487950f3a8eea753cdb4ade39c798b..fdf1278cd0cf065be4aecd58da59bdac351bd548 100644
--- a/deep_sequencing_unit/dist/etc/service.properties
+++ b/deep_sequencing_unit/dist/etc/service.properties
@@ -124,3 +124,5 @@ flow-cell.type-extractor.is-measured = true
# The storage processor (IStorageProcessor implementation)
flow-cell.storage-processor = ch.ethz.bsse.cisd.dsu.dss.StorageProcessor
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
+flow-cell.storage-processor.flow-line-drop-box-template = data/drop-box-{0}
diff --git a/deep_sequencing_unit/etc/service.properties b/deep_sequencing_unit/etc/service.properties
index b973b46b7e70c1379ca5350fbaa75b417d58c567..9a0d8770e48bcfed6b99fad5ac835c838f79e067 100644
--- a/deep_sequencing_unit/etc/service.properties
+++ b/deep_sequencing_unit/etc/service.properties
@@ -124,3 +124,4 @@ flow-cell.type-extractor.is-measured = true
# The storage processor (IStorageProcessor implementation)
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.flow-line-drop-box-template = targets/playground/drop-box-{0}
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 a06534e63e903ee5ffa0847372ed0d3310cca891..18bd8ea30ac0d25046c2ad4a1e3233cb9543cdcc 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
@@ -22,8 +22,13 @@ import java.util.ArrayList;
import java.util.List;
import java.util.Properties;
+import ch.systemsx.cisd.common.TimingParameters;
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.IFileOperations;
+import ch.systemsx.cisd.common.filesystem.IImmutableCopier;
import ch.systemsx.cisd.common.utilities.PropertyUtils;
import ch.systemsx.cisd.openbis.dss.generic.shared.IPostRegistrationDatasetHandler;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -39,17 +44,21 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
static final String FILE_TYPE = ".srf";
private final MessageFormat flowLineDropBoxTemplate;
+ private final IImmutableCopier copier;
+ private final IFileOperations fileOperations;
+ private final List<File> flowLineDataSets = new ArrayList<File>();
FlowLineFeeder(Properties properties)
{
flowLineDropBoxTemplate =
new MessageFormat(PropertyUtils.getMandatoryProperty(properties,
FLOW_LINE_DROP_BOX_TEMPLATE));
+ copier = FastRecursiveHardLinkMaker.tryCreate(TimingParameters.getDefaultParameters());
+ fileOperations = FileOperations.getInstance();
}
public void handle(File originalData, DataSetInformation dataSetInformation)
{
- System.out.println("FlowLineFeeder.handle(): "+originalData+" "+dataSetInformation);
String flowcellID = originalData.getName();
List<File> files = new ArrayList<File>();
findFiles(originalData, files);
@@ -58,20 +67,27 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
String flowLine = extractFlowLine(file);
File dropBox = createDropBoxFile(flowLine);
File flowLineDataSet = new File(dropBox, flowcellID + "_" + flowLine);
+ flowLineDataSets.add(flowLineDataSet);
boolean success = flowLineDataSet.mkdir();
if (success == false)
{
throw new EnvironmentFailureException("Couldn't create folder '"
+ flowLineDataSet.getAbsolutePath() + "'.");
}
-
+ 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() + "'.");
+ }
}
}
private File createDropBoxFile(String flowLine)
{
- File dropBox = new File(flowLineDropBoxTemplate.format(flowLine));
+ File dropBox = new File(flowLineDropBoxTemplate.format(new Object[] {flowLine}));
if (dropBox.exists() == false)
{
throw new ConfigurationFailureException("Drop box '" + dropBox + "' does not exist.");
@@ -86,12 +102,7 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
private String extractFlowLine(File file)
{
String name = file.getName();
- int lastIndexOfDot = name.lastIndexOf('.');
- String nameWithoutType = name;
- if (lastIndexOfDot >= 0)
- {
- nameWithoutType = name.substring(0, lastIndexOfDot);
- }
+ String nameWithoutType = name.substring(0, name.lastIndexOf('.'));
int lastIndexOfUnderScore = nameWithoutType.lastIndexOf('_');
String flowLine = nameWithoutType;
if (lastIndexOfUnderScore >= 0)
@@ -118,7 +129,10 @@ class FlowLineFeeder implements IPostRegistrationDatasetHandler
public void undoLastOperation()
{
- System.out.println("FlowLineFeeder.undoLastOperation()");
+ for (File file : flowLineDataSets)
+ {
+ fileOperations.deleteRecursively(file);
+ }
}
}
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
new file mode 100644
index 0000000000000000000000000000000000000000..1c728db677aeea052ce4d920b7cf2b4020e6ed59
--- /dev/null
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLineFeederTest.java
@@ -0,0 +1,135 @@
+/*
+ * Copyright 2009 ETH Zuerich, CISD
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ * http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+package ch.ethz.bsse.cisd.dsu.dss;
+
+import java.io.File;
+import java.io.IOException;
+import java.util.Properties;
+
+import org.testng.annotations.BeforeMethod;
+import org.testng.annotations.Test;
+
+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;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FlowLineFeederTest extends AbstractFileSystemTestCase
+{
+ private static final String DROP_BOX_PREFIX = "drop-box-";
+ private FlowLineFeeder flowLineFeeder;
+
+ @Override
+ @BeforeMethod
+ public void setUp() throws IOException
+ {
+ super.setUp();
+ 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);
+ }
+
+ @Test
+ public void testMissingProperty()
+ {
+ try
+ {
+ new FlowLineFeeder(new Properties());
+ fail("ConfigurationFailureException expected");
+ } catch (ConfigurationFailureException ex)
+ {
+ assertEquals("Given key '" + FlowLineFeeder.FLOW_LINE_DROP_BOX_TEMPLATE
+ + "' not found in properties '[]'", ex.getMessage());
+ }
+ }
+
+ @Test
+ void testMissingDropBox()
+ {
+ File flowCell = new File(workingDirectory, "abc");
+ assertEquals(true, flowCell.mkdir());
+ FileUtilities.writeToFile(new File(flowCell, "s_3.srf"), "hello flow line 3");
+
+ try
+ {
+ flowLineFeeder.handle(flowCell, null);
+ fail("ConfigurationFailureException expected");
+ } catch (ConfigurationFailureException ex)
+ {
+ AssertionUtil.assertContains(DROP_BOX_PREFIX + "3", ex.getMessage());
+ }
+ }
+
+ @Test
+ public void testHappyCase()
+ {
+ File flowCell = new File(workingDirectory, "abc");
+ 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 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");
+
+ flowLineFeeder.handle(flowCell, null);
+
+ checkFlowLineDataSet(originalFlowLine1, "1");
+ checkFlowLineDataSet(originalFlowLine2, "2");
+ }
+
+ @Test
+ public void testUndoLastOperation()
+ {
+ testHappyCase();
+ assertEquals(1, new File(workingDirectory, DROP_BOX_PREFIX + "1").list().length);
+ assertEquals(1, new File(workingDirectory, DROP_BOX_PREFIX + "2").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);
+ }
+
+ private void checkFlowLineDataSet(File originalFlowLine, String flowLineNumber)
+ {
+ File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLineNumber);
+ File ds = new File(dropBox, "abc_" + flowLineNumber);
+ assertEquals(true, ds.isDirectory());
+
+ File flowLine = new File(ds, originalFlowLine.getName());
+ 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());
+ }
+}