LMS-1035 1) check whether a sample name is in fact a sample code 2) add...

LMS-1035 1) check whether a sample name is in fact a sample code 2) add property holding the original dataset name

SVN: 11731

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/AbstractDelegatingDataSetInfoExtractor.java

+/*
+ * 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);
+    }
+}

rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DataSetInfoExtractorFileNameDecorator.java

+/*
+ * 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());
+    }
+}

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)
         {