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 b3aa091834fd750dd2abc932e7091c472c6ce227..2cf31a6d8b071cd09a9bbce9f712cc0c4c90457e 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
@@ -41,6 +41,7 @@ import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.common.string.UnicodeUtils;
import ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrationGlobalState.SampleRegistrationMode;
import ch.systemsx.cisd.etlserver.entityregistration.SampleDataSetPair.SampleDataSetPairProcessing;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@@ -129,6 +130,18 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
return dataSetType;
}
+ public DataSetKind tryDataSetKind()
+ {
+ String dataSetKindString =
+ properties
+ .tryGet(SampleAndDataSetRegistrationHandler.DATA_SET_KIND_CONTROL_FILE_KEY);
+ if (null == dataSetKindString)
+ {
+ return null;
+ }
+ return DataSetKind.valueOf(dataSetKindString);
+ }
+
public String tryUserString()
{
return properties.tryGet(SampleAndDataSetRegistrationHandler.USER_CONTROL_FILE_KEY);
@@ -199,6 +212,16 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
return dataSetType;
}
+ public DataSetKind getDataSetKind()
+ {
+ DataSetKind dataSetKind = overrideProperties.tryDataSetKind();
+ if (null == dataSetKind)
+ {
+ dataSetKind = globalProperties.tryDataSetKind();
+ }
+ return dataSetKind;
+ }
+
public Person getUser()
{
return user;
@@ -258,7 +281,7 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
BisTabFileLoader<SampleDataSetPair> controlFileLoader =
new BisTabFileLoader<SampleDataSetPair>(
SampleDataSetPairParserObjectFactory.createFactoryFactory(
- properties.getSampleType(), properties.getDataSetType()), false);
+ properties.getSampleType(), properties.getDataSetType(), properties.getDataSetKind()), false);
List<SampleDataSetPair> loadedSampleDataSetPairs = null;
@@ -471,9 +494,9 @@ class SampleAndDataSetControlFileProcessor extends AbstractSampleAndDataSetProce
{
String message =
String.format(
- "Global properties extracted from file '%s': SAMPLE_TYPE(%s) DATA_SET_TYPE(%s) USER(%s)",
+ "Global properties extracted from file '%s': SAMPLE_TYPE(%s) DATA_SET_TYPE(%s) DATA_SET_KIND(%s) USER(%s)",
controlFile.getName(), overrideProperties.trySampleType(),
- overrideProperties.tryDataSetType(), overrideProperties.tryUserString());
+ overrideProperties.tryDataSetType(), overrideProperties.tryDataSetKind(), overrideProperties.tryUserString());
logInfo(message);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationGlobalState.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationGlobalState.java
index 0ff1e3d389fe8d98446627c41204dd5f50b4cd9c..c7ab280a31e31f6601db994d93ccabd429d5d5c0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationGlobalState.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationGlobalState.java
@@ -25,6 +25,7 @@ import ch.systemsx.cisd.common.mail.EMailAddress;
import ch.systemsx.cisd.common.mail.IMailClient;
import ch.systemsx.cisd.etlserver.IDataSetHandler;
import ch.systemsx.cisd.openbis.dss.generic.shared.IEncapsulatedOpenBISService;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.Person;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
@@ -52,6 +53,8 @@ class SampleAndDataSetRegistrationGlobalState
private final DataSetType dataSetTypeOrNull;
+ private final DataSetKind dataSetKindOrNull;
+
private final SampleRegistrationMode sampleRegistrationMode;
private final List<String> errorEmailRecipientsOrNull;
@@ -70,7 +73,7 @@ class SampleAndDataSetRegistrationGlobalState
SampleAndDataSetRegistrationGlobalState(IDataSetHandler delegator,
IEncapsulatedOpenBISService openbisService, SpaceIdentifier spaceIdentifierOrNull,
- SampleType sampleTypeOrNull, DataSetType dataSetTypeOrNull,
+ SampleType sampleTypeOrNull, DataSetType dataSetTypeOrNull, DataSetKind dataSetKindOrNull,
SampleRegistrationMode sampleRegistrationMode, List<String> errorEmailRecipientsOrNull,
String controlFilePattern, boolean alwaysCleanupAfterProcessing,
boolean unmentionedSubfolderIsFailure, boolean useIsFinishedMarkerFile, Logger operationLog)
@@ -80,6 +83,7 @@ class SampleAndDataSetRegistrationGlobalState
this.spaceIdentifierOrNull = spaceIdentifierOrNull;
this.sampleTypeOrNull = sampleTypeOrNull;
this.dataSetTypeOrNull = dataSetTypeOrNull;
+ this.dataSetKindOrNull = dataSetKindOrNull;
this.sampleRegistrationMode = sampleRegistrationMode;
this.errorEmailRecipientsOrNull = errorEmailRecipientsOrNull;
this.controlFilePattern = controlFilePattern;
@@ -128,6 +132,11 @@ class SampleAndDataSetRegistrationGlobalState
return dataSetTypeOrNull;
}
+ public DataSetKind tryDataSetKind()
+ {
+ return dataSetKindOrNull;
+ }
+
public SampleRegistrationMode getSampleRegistrationMode()
{
return sampleRegistrationMode;
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
index 6398338226e4b4f98dcb93b10bd88e9ddd161fa1..7a2033294e2cf74c4e898989a89493b6c0418ad2 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrationHandler.java
@@ -37,6 +37,7 @@ import ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistratio
import ch.systemsx.cisd.etlserver.registrator.MarkerFileUtility;
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.basic.dto.DataSetKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.SampleType;
import ch.systemsx.cisd.openbis.generic.shared.dto.identifier.SpaceIdentifier;
@@ -58,8 +59,12 @@ public class SampleAndDataSetRegistrationHandler implements IDataSetHandlerWithM
static final String DATA_SET_TYPE_CONTROL_FILE_KEY = "DATA_SET_TYPE";
+ static final String DATA_SET_KIND_CONTROL_FILE_KEY = "DATA_SET_KIND";
+
static final String DATA_SET_TYPE_PROPERTIES_KEY = "data-set-type";
+ static final String DATA_SET_KIND_PROPERTIES_KEY = "data-set-kind";
+
static final String SAMPLE_REGISTRATION_MODE_PROPERTIES_KEY = "sample-registration-mode";
static final String USER_CONTROL_FILE_KEY = "USERID";
@@ -126,6 +131,14 @@ public class SampleAndDataSetRegistrationHandler implements IDataSetHandlerWithM
dataSetTypeOrNull.setCode(dataSetTypeCodeOrNull);
}
+ String dataSetKindStringOrNull =
+ PropertyUtils.getProperty(specificProperties, DATA_SET_KIND_PROPERTIES_KEY);
+ DataSetKind dataSetKindOrNull = null;
+ if (null != dataSetKindStringOrNull)
+ {
+ dataSetKindOrNull = DataSetKind.valueOf(dataSetKindStringOrNull);
+ }
+
String sampleRegistrationModeStringOrNull =
PropertyUtils.getProperty(specificProperties,
SAMPLE_REGISTRATION_MODE_PROPERTIES_KEY);
@@ -161,7 +174,7 @@ public class SampleAndDataSetRegistrationHandler implements IDataSetHandlerWithM
((IExtensibleDataSetHandler) delegator).isUseIsFinishedMarkerFile();
return new SampleAndDataSetRegistrationGlobalState(delegator, service, spaceIdentifier,
- sampleTypeOrNull, dataSetTypeOrNull, registrationMode, errorEmailRecipients,
+ sampleTypeOrNull, dataSetTypeOrNull, dataSetKindOrNull, registrationMode, errorEmailRecipients,
controlFilePattern, deleteFilesOnFailure, unmentionedSubfolderIsFailure,
userFinishedMarkerFile, operationLog);
}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
index e40c95b348040caa73a76648b513d57f224ebed3..0a2229924bf700c586734632025f7d97a41c86b5 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleAndDataSetRegistrator.java
@@ -260,6 +260,10 @@ class SampleAndDataSetRegistrator extends AbstractSampleAndDataSetProcessor impl
data.setFileFormatType(fileFormatType);
}
+ if (null != data.getDataSetKind())
+ {
+ data.setDataSetKind(data.getDataSetKind());
+ }
}
/**
diff --git a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java
index 471089f79cc3f4ee04ab0e53cbec64851c7fc755..f45327a6a9a45d7770e82b9e6a01023b71f353c4 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactory.java
@@ -28,6 +28,7 @@ import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.IPropertyModel;
import ch.systemsx.cisd.common.parser.ParserException;
import ch.systemsx.cisd.openbis.dss.generic.shared.dto.DataSetInformation;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetKind;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataSetType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DataTypeCode;
@@ -54,7 +55,7 @@ class SampleDataSetPairParserObjectFactory extends AbstractParserObjectFactory<S
* Clients use the factory factory to make a SampleDataSetPairParserObjectFactory.
*/
public static IParserObjectFactoryFactory<SampleDataSetPair> createFactoryFactory(
- final SampleType sampleType, final DataSetType dataSetType)
+ final SampleType sampleType, final DataSetType dataSetType, DataSetKind dataSetKind)
{
IParserObjectFactoryFactory<SampleDataSetPair> factoryFactory =
new IParserObjectFactoryFactory<SampleDataSetPair>()
@@ -64,7 +65,7 @@ class SampleDataSetPairParserObjectFactory extends AbstractParserObjectFactory<S
final IPropertyMapper propertyMapper) throws ParserException
{
return new SampleDataSetPairParserObjectFactory(sampleType,
- dataSetType, propertyMapper);
+ dataSetType, dataSetKind, propertyMapper);
}
};
@@ -75,17 +76,20 @@ class SampleDataSetPairParserObjectFactory extends AbstractParserObjectFactory<S
private final DataSetType dataSetType;
+ private final DataSetKind dataSetKind;
+
/**
* Clients should use the factory factory to create the factory.
*
* @param propertyMapper
*/
- private SampleDataSetPairParserObjectFactory(SampleType sampleType, DataSetType dataSetType,
+ private SampleDataSetPairParserObjectFactory(SampleType sampleType, DataSetType dataSetType, DataSetKind dataSetKind,
IPropertyMapper propertyMapper)
{
super(SampleDataSetPair.class, propertyMapper);
this.sampleType = sampleType;
this.dataSetType = dataSetType;
+ this.dataSetKind = dataSetKind;
}
private final PropertyType createPropertyType(final String propertyTypeCode)
@@ -218,5 +222,6 @@ class SampleDataSetPairParserObjectFactory extends AbstractParserObjectFactory<S
{
DataSetInformation dataSetInformation = newSampleDataSet.getDataSetInformation();
dataSetInformation.setDataSetType(dataSetType);
+ dataSetInformation.setDataSetKind(dataSetKind);
}
}
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 f5d447d77ed256fc7b33b8649b0ac6de1bc4ac37..da625fa5cda55536cd5697b01da163596cae4c09 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 +17,7 @@
package ch.systemsx.cisd.etlserver.entityregistration;
import static ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrationHandler.DATA_SET_TYPE_PROPERTIES_KEY;
+import static ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrationHandler.DATA_SET_KIND_PROPERTIES_KEY;
import static ch.systemsx.cisd.etlserver.entityregistration.SampleAndDataSetRegistrationHandler.SAMPLE_TYPE_PROPERTIES_KEY;
import java.io.File;
@@ -137,9 +138,9 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(markerFile);
String logText =
- "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) 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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]\n"
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) DATA_SET_KIND(PHYSICAL) 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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]\n"
+ "Encountered errors in the following lines:\n"
+ "# Illegal empty identifier\n"
+ "\t/MYSPACE/MYPROJ/EXP2\tVAL11\tVAL21\tVAL31\tFILE_TYPE\tVAL41\tVAL51\tds2/\n\n"
@@ -177,8 +178,8 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(markerFile);
String logText =
- "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) 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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;Is complete::U]\n"
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) DATA_SET_KIND(PHYSICAL) 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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;Is complete::U]\n"
+ "The following subfolders were in the uploaded folder, but were not mentioned in the control file:\n"
+ "ds2,ds3\n"
+ "The following lines were successfully processed:\n"
@@ -215,10 +216,10 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(markerFile);
String logText =
- "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) 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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) DATA_SET_KIND(PHYSICAL) 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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
@@ -249,14 +250,15 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
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");
+ props.put(HANDLER_PROP_PREFIX + DATA_SET_KIND_PROPERTIES_KEY, "PHYSICAL");
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;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;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;Is complete::U]";
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(null) DATA_SET_TYPE(null) DATA_SET_KIND(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;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;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;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;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;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
@@ -288,10 +290,10 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(markerFile);
String logText =
- "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) 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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) DATA_SET_KIND(PHYSICAL) 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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
@@ -324,10 +326,10 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(markerFile);
String logText =
- "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) USER(test@test.test)\n"
- + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=User::test;Data Set Type::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;Is complete::U]\n"
- + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=User::test;Data Set Type::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;Is complete::U]\n"
- + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=User::test;Data Set Type::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) DATA_SET_KIND(PHYSICAL) USER(test@test.test)\n"
+ + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S1,sampleProperties={prop1: VAL10,prop2: VAL20,prop3: VAL30},dataSetInformation=User::test;Data Set Type::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;Is complete::U]\n"
+ + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=User::test;Data Set Type::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;Is complete::U]\n"
+ + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S3,sampleProperties={prop1: VAL12,prop2: VAL22,prop3: VAL32},dataSetInformation=User::test;Data Set Type::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
@@ -363,10 +365,10 @@ public class SampleAndDatasetRegistrationHandlerTest extends AbstractFileSystemT
handler.handleDataSet(markerFile);
String logText =
- "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) 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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;Is complete::U]\n"
- + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=User::test;Data Set Type::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;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::MY_DATA_SET_TYPE;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
+ "Global properties extracted from file 'control.tsv': SAMPLE_TYPE(MY_SAMPLE_TYPE) DATA_SET_TYPE(MY_DATA_SET_TYPE) DATA_SET_KIND(PHYSICAL) 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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP1;Is complete::U]\n"
+ + "Updated sample, registered data set SampleDataSetPair[sampleIdentifier=/MYSPACE/S2,sampleProperties={prop1: VAL11,prop2: VAL21,prop3: VAL31},dataSetInformation=User::test;Data Set Type::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP2;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::MY_DATA_SET_TYPE;Data Set Kind::PHYSICAL;Experiment Identifier::/MYSPACE/MYPROJ/EXP3;Is complete::U]";
checkAppenderContent(logText, folderName);
context.assertIsSatisfied();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactoryTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactoryTest.java
index d90ab440de971a8156e99f65574432d593722e8c..f3b2cec0509c991678aeebd99cf81af544fd4e19 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactoryTest.java
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/SampleDataSetPairParserObjectFactoryTest.java
@@ -50,7 +50,7 @@ public class SampleDataSetPairParserObjectFactoryTest extends AssertJUnit
BisTabFileLoader<SampleDataSetPair> controlFileLoader =
new BisTabFileLoader<SampleDataSetPair>(
SampleDataSetPairParserObjectFactory.createFactoryFactory(
- properties.trySampleType(), properties.tryDataSetType()), false);
+ properties.trySampleType(), properties.tryDataSetType(), properties.tryDataSetKind()), false);
Reader reader = UnicodeUtils.createReader(new FileInputStream(controlFile));
Map<String, String> defaults = Collections.emptyMap();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/control.tsv b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/control.tsv
index a8d70ccf5927b1d1155673eb9c0f4d2722d2d386..08f0ed89485d0bf9bc26433f7c38a09633cc7330 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/control.tsv
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/basic-example/control.tsv
@@ -2,6 +2,7 @@
#! GLOBAL_PROPERTIES_START
#! SAMPLE_TYPE = MY_SAMPLE_TYPE
#! DATA_SET_TYPE = MY_DATA_SET_TYPE
+#! DATA_SET_KIND = PHYSICAL
#! USERID = test@test.test
#! GLOBAL_PROPERTIES_END
# Data
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/empty-lines/control.tsv b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/empty-lines/control.tsv
index e7427b6162e3b597a813a5e4e615cb5f99829389..08f0ed89485d0bf9bc26433f7c38a09633cc7330 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/empty-lines/control.tsv
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/empty-lines/control.tsv
@@ -2,6 +2,7 @@
#! GLOBAL_PROPERTIES_START
#! SAMPLE_TYPE = MY_SAMPLE_TYPE
#! DATA_SET_TYPE = MY_DATA_SET_TYPE
+#! DATA_SET_KIND = PHYSICAL
#! USERID = test@test.test
#! GLOBAL_PROPERTIES_END
# Data
@@ -9,6 +10,3 @@ S_identifier S_experiment S_PROP1 S_PROP2 S_PROP3 D_file_type D_PROP1 D_PROP2 FO
/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/missing-sample-identifier/control.tsv b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/missing-sample-identifier/control.tsv
index ecdd39dda7c59294e29d7e96c7b3ba2f33cd7bb8..eb17f5c601561087ae5feccb750c7b0ca28ed7fb 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/missing-sample-identifier/control.tsv
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/missing-sample-identifier/control.tsv
@@ -2,6 +2,7 @@
#! GLOBAL_PROPERTIES_START
#! SAMPLE_TYPE = MY_SAMPLE_TYPE
#! DATA_SET_TYPE = MY_DATA_SET_TYPE
+#! DATA_SET_KIND = PHYSICAL
#! USERID = test@test.test
#! GLOBAL_PROPERTIES_END
# Data
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/not-all-subfolders-mentioned/control.tsv b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/not-all-subfolders-mentioned/control.tsv
index 7c75791bb13500e9f02aa6bf3df4d88ba5e74cc3..a2ef7162fe2468fbf6967b1d3112801f51770ac2 100644
--- a/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/not-all-subfolders-mentioned/control.tsv
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/etlserver/entityregistration/test-data/not-all-subfolders-mentioned/control.tsv
@@ -2,9 +2,9 @@
#! GLOBAL_PROPERTIES_START
#! SAMPLE_TYPE = MY_SAMPLE_TYPE
#! DATA_SET_TYPE = MY_DATA_SET_TYPE
+#! DATA_SET_KIND = PHYSICAL
#! 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/
-