[SE-255] cifex data set info extractor extension

SVN: 16274

plasmid/dist/etc/service.properties

@@ -46,10 +46,10 @@ notify-successful-registration = false
 server-url = https://localhost:8443/
 
 # The username to use when contacting the openBIS server
-username = etlserver
+username = etlserver_csb
 
 # The password to use when contacting the openBIS server
-password = etlserver
+password = etlserver_csb
 
 # The base URL for Web client access.
 download-url = https://localhost:8444
@@ -93,7 +93,7 @@ main-thread.incoming-dir = data/incoming
 main-thread.incoming-data-completeness-condition = auto-detection
 # ---------------- Plugin properties
 # The extractor class to use for code extraction
-main-thread.data-set-info-extractor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidDataSetInfoExtractor
+main-thread.data-set-info-extractor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidDefaultDataSetInfoExtractor
 main-thread.data-set-info-extractor.space-code = YEAST_LAB
 
 # The extractor class to use for type extraction
@@ -111,7 +111,7 @@ main-thread.dataset-handler = ch.ethz.bsse.cisd.plasmid.dss.PlasmidDataSetHandle
 cifex.incoming-dir = data/incoming-cifex
 cifex.incoming-data-completeness-condition = auto-detection
 cifex.delete-unidentified = true
-cifex.data-set-info-extractor = ch.systemsx.cisd.etlserver.cifex.CifexDataSetInfoExtractor
+cifex.data-set-info-extractor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidCifexDataSetInfoExtractor
 cifex.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor
 cifex.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor
 cifex.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor

plasmid/etc/service.properties

@@ -53,10 +53,10 @@ notify-successful-registration = false
 server-url = http://localhost:8888
 
 # The username to use when contacting the openBIS server
-username = etlserver
+username = etlserver_csb
 
 # The password to use when contacting the openBIS server
-password = etlserver
+password = etlserver_csb
 
 # The base URL for Web client access.
 download-url = http://localhost:${port}
@@ -99,7 +99,7 @@ main-thread.incoming-dir = ${data-folder}/incoming
 main-thread.incoming-data-completeness-condition = auto-detection
 # ---------------- Plugin properties
 # The extractor class to use for code extraction
-main-thread.data-set-info-extractor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidDataSetInfoExtractor
+main-thread.data-set-info-extractor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidDefaultDataSetInfoExtractor
 main-thread.data-set-info-extractor.space-code = YEAST_LAB
 
 # The extractor class to use for type extraction
@@ -117,7 +117,7 @@ main-thread.dataset-handler = ch.ethz.bsse.cisd.plasmid.dss.PlasmidDataSetHandle
 cifex.incoming-dir = ${data-folder}/incoming-cifex
 cifex.incoming-data-completeness-condition = auto-detection
 cifex.delete-unidentified = true
-cifex.data-set-info-extractor = ch.systemsx.cisd.etlserver.cifex.CifexDataSetInfoExtractor
+cifex.data-set-info-extractor = ch.ethz.bsse.cisd.plasmid.dss.PlasmidCifexDataSetInfoExtractor
 cifex.type-extractor = ch.systemsx.cisd.etlserver.cifex.CifexTypeExtractor
 cifex.storage-processor = ch.systemsx.cisd.etlserver.CifexStorageProcessor
 cifex.storage-processor.processor = ch.systemsx.cisd.etlserver.DefaultStorageProcessor

plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/DataSetFileNamePropertyHelper.java

+/*
+ * 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.plasmid.dss;
+
+import java.io.File;
+
+import org.apache.commons.io.FilenameUtils;
+
+import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
+
+/**
+ * Helper class for creation of data set property of type {@code FILE_NAME} holding name of the file
+ * stored for the data set.
+ * 
+ * @author Piotr Buczek
+ */
+class DataSetFileNamePropertyHelper
+{
+    private final static String FILE_NAME_PROPERTY = "FILE_NAME";
+
+    static NewProperty createProperty(File incomingDataSetFile, boolean stripExtension)
+    {
+        String fileName = incomingDataSetFile.getName();
+        if (stripExtension)
+        {
+            fileName = FilenameUtils.removeExtension(fileName);
+        }
+        return new NewProperty(FILE_NAME_PROPERTY, fileName);
+    }
+
+}

plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidCifexDataSetInfoExtractor.java

+/*
+ * 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.plasmid.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.IDataSetInfoExtractor;
+import ch.systemsx.cisd.etlserver.cifex.CifexDataSetInfoExtractor;
+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;
+
+/**
+ * {@link IDataSetInfoExtractor} implementation that delegates extraction of data to
+ * {@link CifexDataSetInfoExtractor} and adds one property of type {@code FILE_NAME} holding name of
+ * the file stored for the data set. Registration will fail if this property type doesn't exist in
+ * openBIS DB or is not attached to the data set type extracted by type extractor.
+ * 
+ * @author Piotr Buczek
+ */
+public class PlasmidCifexDataSetInfoExtractor implements IDataSetInfoExtractor
+{
+    private final IDataSetInfoExtractor delegator;
+
+    public PlasmidCifexDataSetInfoExtractor(final Properties globalProperties)
+    {
+        this.delegator = new CifexDataSetInfoExtractor(globalProperties);
+    }
+
+    public DataSetInformation getDataSetInformation(File incomingDataSetFile,
+            IEncapsulatedOpenBISService openbisService) throws UserFailureException,
+            EnvironmentFailureException
+    {
+        final DataSetInformation result =
+                delegator.getDataSetInformation(incomingDataSetFile, openbisService);
+        final NewProperty fileNameProperty =
+                DataSetFileNamePropertyHelper.createProperty(incomingDataSetFile, true);
+        result.getDataSetProperties().add(fileNameProperty);
+        return result;
+    }
+}

plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidDataSetInfoExtractor.java → plasmid/source/java/ch/ethz/bsse/cisd/plasmid/dss/PlasmidDefaultDataSetInfoExtractor.java

@@ -35,17 +35,15 @@ import ch.systemsx.cisd.openbis.generic.shared.dto.NewProperty;
  * <p>
  * Registered data sets will have one property of type {@code FILE_NAME} holding name of the file
  * stored for the data set. Registration will fail if this property type doesn't exist in openBIS DB
- * or is not attached to the data set type extracted by {@link PlasmidTypeExtractor}.
+ * or is not attached to the data set type extracted by type extractor.
  * 
  * @author Piotr Buczek
  */
-public class PlasmidDataSetInfoExtractor implements IDataSetInfoExtractor
+public class PlasmidDefaultDataSetInfoExtractor implements IDataSetInfoExtractor
 {
-    private final static String FILE_NAME_PROPERTY = "FILE_NAME";
-
     private final IDataSetInfoExtractor delegator;
 
-    public PlasmidDataSetInfoExtractor(final Properties globalProperties)
+    public PlasmidDefaultDataSetInfoExtractor(final Properties globalProperties)
     {
         this.delegator = new DefaultDataSetInfoExtractor(globalProperties);
     }
@@ -57,8 +55,9 @@ public class PlasmidDataSetInfoExtractor implements IDataSetInfoExtractor
         final DataSetInformation result =
                 delegator
                         .getDataSetInformation(incomingDataSetFile.getParentFile(), openbisService);
-        result.getDataSetProperties().add(
-                new NewProperty(FILE_NAME_PROPERTY, incomingDataSetFile.getName()));
+        final NewProperty fileNameProperty =
+                DataSetFileNamePropertyHelper.createProperty(incomingDataSetFile, false);
+        result.getDataSetProperties().add(fileNameProperty);
         return result;
     }
 }