diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/AbstractDelegatingDataSetInfoExtractor.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/AbstractDelegatingDataSetInfoExtractor.java
new file mode 100644
index 0000000000000000000000000000000000000000..2a198aae9f64e36c1967d8df07521219d7040609
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/AbstractDelegatingDataSetInfoExtractor.java
@@ -0,0 +1,104 @@
+/*
+ * Copyright 2007 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.systemsx.cisd.yeastx.etl;
+
+import java.io.File;
+import java.util.Properties;
+
+import org.apache.log4j.Logger;
+
+import ch.rinn.restrictions.Private;
+import ch.systemsx.cisd.common.exceptions.ConfigurationFailureException;
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+import ch.systemsx.cisd.common.utilities.ClassUtils;
+import ch.systemsx.cisd.common.utilities.ExtendedProperties;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+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;
+
+/**
+ * DataSetInfoExtractor which delegates all the tasks to the instance specified in configuration
+ * with {@link #DELEGATOR_CLASS_PROPERTY} property.
+ * <p>
+ * This class is supposed to be extended to add specific functionality which has to be performed
+ * besides the basic operations.
+ * </p>
+ *
+ * @author Tomasz Pylak
+ */
+// TODO 2009-07-13, Tomasz Pylak: move to datastore_server project at the end of the sprint
+abstract public class AbstractDelegatingDataSetInfoExtractor implements IDataSetInfoExtractor
+{
+ /**
+ * Property name which is used to specify the class of the default data set info extractor, to
+ * which all calls are delegated.
+ */
+ public final static String DELEGATOR_CLASS_PROPERTY = "delegator";
+
+ final static Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION,
+ AbstractDelegatingDataSetInfoExtractor.class);
+
+ private final IDataSetInfoExtractor delegator;
+
+ protected AbstractDelegatingDataSetInfoExtractor(Properties properties)
+ {
+ this(createDelegator(properties));
+ }
+
+ protected AbstractDelegatingDataSetInfoExtractor(IDataSetInfoExtractor delegator)
+ {
+ this.delegator = delegator;
+ }
+
+ @Private
+ static IDataSetInfoExtractor createDelegator(Properties properties)
+ {
+ String delegateClass =
+ PropertyUtils.getMandatoryProperty(properties, DELEGATOR_CLASS_PROPERTY);
+ Properties p =
+ ExtendedProperties.getSubset(properties, DELEGATOR_CLASS_PROPERTY + ".", true);
+ return createClass(IDataSetInfoExtractor.class, delegateClass, p);
+ }
+
+ private final static <T> T createClass(final Class<T> superClazz, String className,
+ Object... argumentsOrNull)
+ {
+ try
+ {
+ return ClassUtils.create(superClazz, className, argumentsOrNull);
+ } catch (IllegalArgumentException ex)
+ {
+ throw new ConfigurationFailureException(ex.getMessage());
+ }
+ }
+
+ //
+ // delegation
+ //
+
+ public DataSetInformation getDataSetInformation(File incomingDataSetPath,
+ IEncapsulatedOpenBISService openbisService) throws UserFailureException,
+ EnvironmentFailureException
+ {
+ return delegator.getDataSetInformation(incomingDataSetPath, openbisService);
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetInfoExtractorFileNameDecorator.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetInfoExtractorFileNameDecorator.java
new file mode 100644
index 0000000000000000000000000000000000000000..c3ee5a4147100091bca57329a6ee78b2fc79ad71
--- /dev/null
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetInfoExtractorFileNameDecorator.java
@@ -0,0 +1,71 @@
+/*
+ * 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.systemsx.cisd.yeastx.etl;
+
+import java.io.File;
+import java.util.List;
+import java.util.Properties;
+
+import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.utilities.PropertyUtils;
+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.NewProperty;
+
+/**
+ * Uses a delegator extractor specified at {@link #DELEGATOR_CLASS_PROPERTY} property and enriches
+ * the extracted information by adding a dataset property with a file name of the original dataset.
+ * The name of the property used for the file name must be specified in
+ * {@link #FILE_NAME_PROPERTY_NAME} property.
+ *
+ * @author Tomasz Pylak
+ */
+public class DataSetInfoExtractorFileNameDecorator extends AbstractDelegatingDataSetInfoExtractor
+{
+ /**
+ * Name of the property, which holds the property code in the database, at which the original
+ * dataset file name should be stored.
+ */
+ public static final String FILE_NAME_PROPERTY_NAME = "file-name-property-code";
+
+ private final String fileNamePropertyCode;
+
+ public DataSetInfoExtractorFileNameDecorator(Properties properties)
+ {
+ super(properties);
+ String code = PropertyUtils.getMandatoryProperty(properties, FILE_NAME_PROPERTY_NAME);
+ this.fileNamePropertyCode = DatasetMappingResolver.adaptPropertyCode(code);
+ }
+
+ @Override
+ public DataSetInformation getDataSetInformation(File incomingDataSetPath,
+ IEncapsulatedOpenBISService openbisService) throws UserFailureException,
+ EnvironmentFailureException
+ {
+ DataSetInformation info = super.getDataSetInformation(incomingDataSetPath, openbisService);
+ List<NewProperty> properties = info.getDataSetProperties();
+ properties.add(createFileNameProperty(incomingDataSetPath));
+ info.setDataSetProperties(properties);
+ return info;
+ }
+
+ private NewProperty createFileNameProperty(File incomingDataSetPath)
+ {
+ return new NewProperty(fileNamePropertyCode, incomingDataSetPath.getName());
+ }
+}
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
index 6c7dadc3bf87cdfe159164ebb2db788a442cdb29..1760f9c7266694f5276887d7d28dec32702711d0 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
@@ -130,28 +130,27 @@ class DatasetMappingResolver
return sampleCodeOrLabel;
}
}
- LocalExperimentIdentifier experimentIdentifier =
- tryGetExperimentIdentifier(mapping, experimentPropertyCodeOrNull);
ListSamplesByPropertyCriteria criteria =
- new ListSamplesByPropertyCriteria(samplePropertyCodeOrNull, sampleCodeOrLabel,
- mapping.getGroupCode(), experimentIdentifier);
- List<String> samples;
- try
+ createFindSampleByNameCriteria(mapping, sampleCodeOrLabel);
+ List<String> samples = tryListSamplesByCriteria(criteria, mapping, log);
+ if (samples == null)
{
- samples = openbisService.listSamplesByCriteria(criteria);
- } catch (UserFailureException e)
- {
- log.datasetMappingError(mapping, e.getMessage());
- return null;
- }
- if (samples.size() == 1)
+ return null; // some error occurred
+ } else if (samples.size() == 1)
{
return samples.get(0);
} else if (samples.size() == 0)
{
- log.datasetMappingError(mapping, "there is no sample which matches the criteria <"
- + criteria + ">");
- return null;
+ // try to assume that the sample code, not name, has been provided
+ if (isConnectedToExperiment(sampleCodeOrLabel, mapping, log))
+ {
+ return sampleCodeOrLabel;
+ } else
+ {
+ log.datasetMappingError(mapping, "there is no sample which matches the criteria <"
+ + criteria + ">");
+ return null;
+ }
} else
{
String errMsg =
@@ -164,6 +163,30 @@ class DatasetMappingResolver
}
}
+ private List<String> tryListSamplesByCriteria(ListSamplesByPropertyCriteria criteria,
+ DataSetMappingInformation mapping, LogUtils log)
+ {
+ try
+ {
+ return openbisService.listSamplesByCriteria(criteria);
+ } catch (UserFailureException e)
+ {
+ log.datasetMappingError(mapping, e.getMessage());
+ return null;
+ }
+ }
+
+ private ListSamplesByPropertyCriteria createFindSampleByNameCriteria(
+ DataSetMappingInformation mapping, String sampleCodeOrLabel)
+ {
+ LocalExperimentIdentifier experimentIdentifier =
+ tryGetExperimentIdentifier(mapping, experimentPropertyCodeOrNull);
+ ListSamplesByPropertyCriteria criteria =
+ new ListSamplesByPropertyCriteria(samplePropertyCodeOrNull, sampleCodeOrLabel,
+ mapping.getGroupCode(), experimentIdentifier);
+ return criteria;
+ }
+
private static LocalExperimentIdentifier tryGetExperimentIdentifier(
DataSetMappingInformation mapping, String experimentPropertyCodeOrNull)
{
@@ -315,7 +338,7 @@ class DatasetMappingResolver
return properties;
}
- private static String adaptPropertyCode(String propertyCode)
+ public static String adaptPropertyCode(String propertyCode)
{
if (propertyCode.toLowerCase().startsWith(PROPERTIES_PREFIX.toLowerCase()) == false)
{