LMS-1502 Working on extractors for CINA Metadata from XML files.

SVN: 16285

rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/BundleMetadataExtractor.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.systemsx.cisd.cina.shared.metadata;
+
+/**
+ * 
+ *
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class BundleMetadataExtractor
+{
+    
+}

rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractor.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.systemsx.cisd.cina.shared.metadata;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+
+import ch.systemsx.cisd.cina.shared.labview.Cluster;
+import ch.systemsx.cisd.cina.shared.labview.LVData;
+import ch.systemsx.cisd.cina.shared.labview.LVDataParser;
+import ch.systemsx.cisd.cina.shared.labview.LVDataString;
+
+/**
+ * Class for extracting the metadata from a folder containing an image + metadata.
+ * 
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ImageMetadataExtractor
+{
+    private final Map<String, String> metadata;
+
+    private final File folder;
+
+    private static final String METADATA_FILE_NAME = "metadata.xml";
+
+    /**
+     * Create an image metadata with a parent metadata.
+     * 
+     * @param parentMetadata The inherited parent metadata
+     * @param folder The folder containing the metadata
+     */
+    public ImageMetadataExtractor(Map<String, String> parentMetadata, File folder)
+    {
+        this.metadata = new HashMap<String, String>(parentMetadata);
+        this.folder = folder;
+    }
+
+    public Map<String, String> getMetadata()
+    {
+        return metadata;
+    }
+
+    public void parse()
+    {
+        File metadataFile = new File(folder, METADATA_FILE_NAME);
+        LVData lvdata = LVDataParser.parse(metadataFile);
+        if (null == lvdata)
+        {
+            throw new IllegalArgumentException("Could not parse metadata in file "
+                    + metadataFile.getAbsolutePath());
+        }
+
+        if (1 != lvdata.getClusters().size())
+        {
+            throw new IllegalArgumentException("Parser expects only one cluster in file "
+                    + metadataFile.getAbsolutePath() + "; Found " + lvdata.getClusters().size());
+        }
+
+        Cluster cluster = lvdata.getClusters().get(0);
+        List<LVDataString> lvdataStrings = cluster.getStrings();
+        for (LVDataString lvdataString : lvdataStrings)
+        {
+            metadata.put(lvdataString.getName(), lvdataString.getValue());
+        }
+    }
+}

rtd_cina/source/java/ch/systemsx/cisd/cina/shared/metadata/ReplicaMetadataExtractor.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.systemsx.cisd.cina.shared.metadata;
+
+//import java.io.File;
+//import java.util.ArrayList;
+//import java.util.List;
+//import java.util.Map;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ReplicaMetadataExtractor
+{
+    // private final List<Map<String, String>> metadata;
+    //
+    // private final File folder;
+    //
+    // public ReplicaMetadataExtractor()
+    // {
+    // metadata = new ArrayList<Map<String, String>>();
+    // folder = null;
+    // }
+}

rtd_cina/sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/ImageMetadataExtractorTest.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.systemsx.cisd.cina.shared.metadata;
+
+import java.io.File;
+import java.util.HashMap;
+import java.util.Map;
+
+import org.testng.AssertJUnit;
+import org.testng.annotations.Test;
+
+/**
+ * @author Chandrasekhar Ramakrishnan
+ */
+public class ImageMetadataExtractorTest extends AssertJUnit
+{
+    @Test
+    public void testMetadataExtraction()
+    {
+        HashMap<String, String> parentMetadata = new HashMap<String, String>();
+        File folder =
+                new File(
+                        "sourceTest/java/ch/systemsx/cisd/cina/shared/metadata/Annotations/Replica for MRC files/MRC for Thomas/test20090422_BacklashRef.mrc");
+        ImageMetadataExtractor metadata = new ImageMetadataExtractor(parentMetadata, folder);
+        metadata.parse();
+        Map<String, String> metadataMap = metadata.getMetadata();
+        assertEquals("", metadataMap.get("Annotation"));
+        assertEquals("CM10", metadataMap.get("Microscope"));
+        assertEquals("thomas.braun@unibas.ch", metadataMap.get("Operator"));
+        assertEquals("test20090422_BacklashRef.mrc", metadataMap.get("Filename"));
+    }
+}