diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneDataSetInfoExtractor.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneDataSetInfoExtractor.java
new file mode 100644
index 0000000000000000000000000000000000000000..95a32df99b5e328970d1620c69d9245c732c103f
--- /dev/null
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneDataSetInfoExtractor.java
@@ -0,0 +1,59 @@
+/*
+ * Copyright 2010 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.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.etlserver.DefaultDataSetInfoExtractor;
+import ch.systemsx.cisd.etlserver.IDataSetInfoExtractor;
+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.shared.dto.identifier.SampleIdentifier;
+
+/**
+ * @author Franz-Josef Elmer
+ */
+public class FlowLaneDataSetInfoExtractor implements IDataSetInfoExtractor
+{
+ static final String FLOW_LANE_NUMBER_SEPARATOR = ".";
+
+ private final IDataSetInfoExtractor dataSetInfoExtractor;
+
+ public FlowLaneDataSetInfoExtractor(Properties properties)
+ {
+ dataSetInfoExtractor = new DefaultDataSetInfoExtractor(properties);
+ }
+
+ public DataSetInformation getDataSetInformation(File incomingDataSetPath,
+ IEncapsulatedOpenBISService openbisService) throws UserFailureException,
+ EnvironmentFailureException
+ {
+ DataSetInformation dataSetInformation =
+ dataSetInfoExtractor.getDataSetInformation(incomingDataSetPath, openbisService);
+ String sampleCode = dataSetInformation.getSampleCode();
+ if (sampleCode != null)
+ {
+ dataSetInformation.setSampleCode(sampleCode.replace(FLOW_LANE_NUMBER_SEPARATOR,
+ SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING));
+ }
+ return dataSetInformation;
+ }
+
+}
diff --git a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
index e7afa3d671a78128ab596f1c3989a65116b259e9..61a4bbf3898696d7e23ba1164d8469bfbff45f68 100644
--- a/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
+++ b/deep_sequencing_unit/source/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeeder.java
@@ -160,7 +160,7 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
File dropBox = createDropBoxFile(flowLane);
String fileName =
flowLaneSample.getGroup().getCode() + entitySepaparator + flowcellID
- + SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING + flowLane;
+ + FlowLaneDataSetInfoExtractor.FLOW_LANE_NUMBER_SEPARATOR + flowLane;
File flowLaneDataSet = new File(dropBox, fileName);
if (flowLaneDataSet.exists())
{
@@ -274,8 +274,10 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
builder.append(line).append('\n');
}
}
- String metaFileName = flowLaneSample.getCode() + META_DATA_FILE_TYPE;
- metaFileName = asFileName(metaFileName);
+ String sampleCode = flowLaneSample.getCode();
+ String metaFileName =
+ escapeSampleCode(sampleCode)
+ + META_DATA_FILE_TYPE;
FileUtilities.writeToFile(new File(flowLaneDataSet, metaFileName), builder.toString());
if (dropBox != null)
{
@@ -289,15 +291,10 @@ class FlowLaneFeeder extends AbstractPostRegistrationDataSetHandlerForFileBasedU
}
}
- // TODO : more generic solution for avoiding escape chars in file names, this is just quick and
- // dirty
- static String asFileName(String originalFileName)
+ static String escapeSampleCode(String sampleCode)
{
- String fileName = originalFileName;
- fileName = fileName.replace("/", "_");
- fileName = fileName.replace(":", "_");
- fileName = fileName.replace("\\", "_");
- return fileName;
+ return sampleCode == null ? null : sampleCode.replace(
+ SampleIdentifier.CONTAINED_SAMPLE_CODE_SEPARARTOR_STRING, "_");
}
private void addLine(StringBuilder builder, String key, String value)
diff --git a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
index 6285c73fa5a1a62317fc17d1f6ede322d5e16852..8671932699fd95b9793f758345fd07575ece88a5 100644
--- a/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
+++ b/deep_sequencing_unit/sourceTest/java/ch/ethz/bsse/cisd/dsu/dss/FlowLaneFeederTest.java
@@ -16,7 +16,7 @@
package ch.ethz.bsse.cisd.dsu.dss;
-import static ch.ethz.bsse.cisd.dsu.dss.FlowLaneFeeder.asFileName;
+import static ch.ethz.bsse.cisd.dsu.dss.FlowLaneDataSetInfoExtractor.FLOW_LANE_NUMBER_SEPARATOR;
import java.io.File;
import java.io.FilenameFilter;
@@ -263,10 +263,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
File[] transferedFiles = transferDropBox.listFiles();
assertEquals(1, transferedFiles.length);
- String sampleName = SAMPLE_CODE + ":2";
- assertEquals("G2_" + sampleName, transferedFiles[0].getName());
+ String sampleName = SAMPLE_CODE + FLOW_LANE_NUMBER_SEPARATOR + "2";
+ assertEquals("G2_" + FlowLaneFeeder.escapeSampleCode(sampleName), transferedFiles[0].getName());
File metaFile = getFile(transferedFiles[0], FlowLaneFeeder.META_DATA_FILE_TYPE);
- String myFileName = asFileName(sampleName + FlowLaneFeeder.META_DATA_FILE_TYPE);
+ String myFileName = SAMPLE_CODE + "_2" + FlowLaneFeeder.META_DATA_FILE_TYPE;
assertEquals(myFileName, metaFile.getName());
assertHardLinkOnSameFile(originalFlowLane2, getFile(transferedFiles[0], "2.srf"));
@@ -303,10 +303,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
File[] transferedFiles = transferDropBox.listFiles();
assertEquals(1, transferedFiles.length);
- String sampleName = SAMPLE_CODE + ":2";
+ String sampleName = SAMPLE_CODE + FLOW_LANE_NUMBER_SEPARATOR + "2";
assertEquals("G2_" + sampleName, transferedFiles[0].getName());
File metaFile = getFile(transferedFiles[0], FlowLaneFeeder.META_DATA_FILE_TYPE);
- assertEquals(asFileName(sampleName + FlowLaneFeeder.META_DATA_FILE_TYPE), metaFile
+ assertEquals(SAMPLE_CODE + "_2" + FlowLaneFeeder.META_DATA_FILE_TYPE, metaFile
.getName());
List<String> metaData = FileUtilities.loadToStringList(metaFile);
String lastLine = metaData.remove(metaData.size() - 1);
@@ -352,7 +352,7 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
{
public boolean accept(File dir, String name)
{
- return name.endsWith(fileNameExtension);
+ return FlowLaneFeeder.escapeSampleCode(name).endsWith(FlowLaneFeeder.escapeSampleCode(fileNameExtension));
}
});
assertEquals(1, files.length);
@@ -443,10 +443,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
private GenericValueEntityProperty createProperty(String key, String value)
{
GenericValueEntityProperty p = new GenericValueEntityProperty();
- p.setValue(value);
+ p.setValue(FlowLaneFeeder.escapeSampleCode(value));
PropertyType propertyType = new PropertyType();
- propertyType.setCode(key);
- propertyType.setLabel(key.toLowerCase());
+ propertyType.setCode(FlowLaneFeeder.escapeSampleCode(key));
+ propertyType.setLabel(FlowLaneFeeder.escapeSampleCode(key).toLowerCase());
p.setPropertyType(propertyType);
return p;
}
@@ -455,11 +455,11 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
private void checkFlowLaneDataSet(File originalFlowLane, String flowLaneNumber)
{
- File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + flowLaneNumber);
- String flowLaneSampleCode = SAMPLE_CODE + ":" + flowLaneNumber;
+ File dropBox = new File(workingDirectory, DROP_BOX_PREFIX + FlowLaneFeeder.escapeSampleCode(flowLaneNumber));
String fileName =
- "G" + flowLaneNumber + FlowLaneFeeder.DEFAULT_ENTITY_SEPARATOR + flowLaneSampleCode;
- File ds = new File(dropBox, fileName);
+ "G" + FlowLaneFeeder.escapeSampleCode(flowLaneNumber) + FlowLaneFeeder.DEFAULT_ENTITY_SEPARATOR + SAMPLE_CODE
+ + FLOW_LANE_NUMBER_SEPARATOR + FlowLaneFeeder.escapeSampleCode(flowLaneNumber);
+ File ds = new File(dropBox, FlowLaneFeeder.escapeSampleCode(fileName));
assertEquals(true, ds.isDirectory());
File flowLane = new File(ds, originalFlowLane.getName());
@@ -467,10 +467,10 @@ public class FlowLaneFeederTest extends AbstractFileSystemTestCase
assertEquals(FileUtilities.loadToString(originalFlowLane), FileUtilities
.loadToString(flowLane));
assertHardLinkOnSameFile(originalFlowLane, flowLane);
- String metaDataFileName = flowLaneSampleCode + FlowLaneFeeder.META_DATA_FILE_TYPE;
- metaDataFileName = asFileName(metaDataFileName);
- assertEquals(true, new File(ds, metaDataFileName).exists());
- assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + fileName).exists());
+ String metaDataFileName =
+ (SAMPLE_CODE + "_" + FlowLaneFeeder.escapeSampleCode(flowLaneNumber)) + FlowLaneFeeder.META_DATA_FILE_TYPE;
+ assertEquals(true, new File(ds, FlowLaneFeeder.escapeSampleCode(metaDataFileName)).exists());
+ assertEquals(true, new File(dropBox, Constants.IS_FINISHED_PREFIX + FlowLaneFeeder.escapeSampleCode(fileName)).exists());
}
private void assertHardLinkOnSameFile(File file1, File file2)