diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
index f641a2f71a340560de53bc4510818e48fcb353b8..5066a24b08900235a9e899a55854bc9ac6ea412a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetControlFileProcessor.java
@@ -103,7 +103,7 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
{
String sampleTypeCode =
properties
- .get(SampleAndDataSetRegistrationHandler.SAMPLE_TYPE_CONTROL_FILE_KEY);
+ .tryGet(SampleAndDataSetRegistrationHandler.SAMPLE_TYPE_CONTROL_FILE_KEY);
if (null == sampleTypeCode)
{
return null;
@@ -117,7 +117,7 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
{
String dataSetTypeCode =
properties
- .get(SampleAndDataSetRegistrationHandler.DATA_SET_TYPE_CONTROL_FILE_KEY);
+ .tryGet(SampleAndDataSetRegistrationHandler.DATA_SET_TYPE_CONTROL_FILE_KEY);
if (null == dataSetTypeCode)
{
return null;
@@ -129,7 +129,7 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
public String tryUserString()
{
- return properties.get(SampleAndDataSetRegistrationHandler.USER_CONTROL_FILE_KEY);
+ return properties.tryGet(SampleAndDataSetRegistrationHandler.USER_CONTROL_FILE_KEY);
}
}
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
index 563e416bb370c8bcbc6640ad10ee96282935d8f5..651354882bc2384eb578e6ce00db350fa3f641b6 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDatasetRegistrationHandlerTest.java
@@ -17,6 +17,9 @@
package ch.systemsx.cisd.etlserver.entityregistration;
import static ch.systemsx.cisd.common.Constants.IS_FINISHED_PREFIX;
+import static ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrationHandler.DATA_SET_TYPE_PROPERTIES_KEY;
+import static ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrationHandler.SAMPLE_TYPE_PROPERTIES_KEY;
+
import java.io.File;
import java.io.IOException;
import java.util.Collections;
@@ -43,6 +46,7 @@ import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.common.test.RecordingMatcher;
import ch.systemsx.cisd.etlserver.DataSetRegistrationAlgorithm;
+import ch.systemsx.cisd.etlserver.IDataSetHandler;
import ch.systemsx.cisd.etlserver.IExtensibleDataSetHandler;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
@@ -64,6 +68,8 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
{
private static final String SPACE_CODE = "MYSPACE";
+ private static final String HANDLER_PROP_PREFIX = IDataSetHandler.DATASET_HANDLER_KEY + ".";
+
protected Mockery context;
protected IEncapsulatedOpenBISService openbisService;
@@ -217,6 +223,44 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
context.assertIsSatisfied();
}
+ @Test
+ public void testDefaultSampleAndDataSetTypes()
+ {
+ final RecordingMatcher<DataSetInformation> dataSetInfoMatcher =
+ new RecordingMatcher<DataSetInformation>();
+ final RecordingMatcher<NewSample> newSampleMatcher = new RecordingMatcher<NewSample>();
+
+ setupOpenBisExpectations();
+ NewExternalData externalData = setupDataSetHandlerExpectations(dataSetInfoMatcher, 3);
+ setupUpdateSampleExistsExpectations("S1", false);
+ setupUpdateSampleExistsExpectations("S2", false);
+ setupUpdateSampleExistsExpectations("S3", false);
+ setupRegisterSampleAndDataSetExpectations(externalData, newSampleMatcher, 3);
+
+ final String folderName = "no-global-config";
+ final RecordingMatcher<DataHandler> attachmentMatcher = new RecordingMatcher<DataHandler>();
+ final RecordingMatcher<EMailAddress[]> addressesMatcher =
+ new RecordingMatcher<EMailAddress[]>();
+ setupSuccessEmailExpectations(attachmentMatcher, addressesMatcher, folderName);
+
+ createWorkingCopyOfTestFolder(folderName);
+
+ Properties props = createDefaultHandlerProps();
+ props.put(HANDLER_PROP_PREFIX + SAMPLE_TYPE_PROPERTIES_KEY, "DEF_SAMPLE_TYPE");
+ props.put(HANDLER_PROP_PREFIX + DATA_SET_TYPE_PROPERTIES_KEY, "DEF_DS_TYPE");
+ initializeDataSetHandler(props);
+ handler.handleDataSet(markerFile);
+
+ String logText =
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(null) DATA_SET_TYPE(null) USER(test@test.test)\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=User::test;Data Set Type::DEF_DS_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;Production Date::;Is complete::U]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=User::test;Data Set Type::DEF_DS_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;Production Date::;Is complete::U]\n"
+ + "Registered sample/data set pair SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=User::test;Data Set Type::DEF_DS_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Production Date::;Is complete::U]";
+ checkAppenderContent(logText, folderName);
+
+ context.assertIsSatisfied();
+ }
+
@Test
public void testRegisteringWithEmptyLinesInControlFile()
{
@@ -393,10 +437,16 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
context.assertIsSatisfied();
}
- private void initializeDefaultDataSetHandler()
+ private Properties createDefaultHandlerProps()
{
final Properties props = new Properties();
props.setProperty("dataset-handler.data-space", "store");
+ return props;
+ }
+
+ private void initializeDefaultDataSetHandler()
+ {
+ Properties props = createDefaultHandlerProps();
initializeDataSetHandler(props);
}
@@ -415,7 +465,11 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
workingCopy = new File(workingDirectory, folderName);
FileOperations.getInstance().copy(dataSetFile, workingCopy);
- FileOperations.getInstance().deleteRecursively(new File(workingCopy, ".svn"));
+ final File svnFolder = new File(workingCopy, ".svn");
+ if (svnFolder.exists())
+ {
+ FileOperations.getInstance().deleteRecursively(svnFolder);
+ }
markerFile = new File(workingDirectory, IS_FINISHED_PREFIX + folderName);
FileUtilities.writeToFile(markerFile, "");
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/control.tsv b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/control.tsv
new file mode 100644
index 0000000000000000000000000000000000000000..9aa40df1f2c800b06da6f57f68b9c2560e3dfc3a
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/control.tsv
@@ -0,0 +1,9 @@
+# Control Parameters
+#! GLOBAL_PROPERTIES_START
+#! USERID = test@test.test
+#! GLOBAL_PROPERTIES_END
+# Data
+S_identifier S_experiment S_PROP1 S_PROP2 S_PROP3 D_file_type D_PROP1 D_PROP2 FOLDER
+/MYSPACE/S1 /MYSPACE/MYPROJ/EXP1 VAL10 VAL20 VAL30 FILE_TYPE VAL40 VAL50 ds1/
+/MYSPACE/S2 /MYSPACE/MYPROJ/EXP2 VAL11 VAL21 VAL31 FILE_TYPE VAL41 VAL51 ds2/
+/MYSPACE/S3 /MYSPACE/MYPROJ/EXP3 VAL12 VAL22 VAL32 FILE_TYPE VAL42 VAL52 ds3/
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/ds1/dataset.txt b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/ds1/dataset.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/ds2/dataset.txt b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/ds2/dataset.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/ds3/dataset.txt b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/no-global-config/ds3/dataset.txt
new file mode 100644
index 0000000000000000000000000000000000000000..e69de29bb2d1d6434b8b29ae775ad8c2e48c5391