SE-209 LMC: transformer for analysis data

SVN: 14748

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/ImageAnalysisLMCSplitter.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.openbis.plugin.screening.transformers;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.io.FileOutputStream;
+import java.io.IOException;
+import java.io.OutputStream;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.commons.lang.StringUtils;
+
+import com.csvreader.CsvReader;
+
+/**
+ * Splits a file with image analysis results for all plates into a set of files, one for each plate.
+ * 
+ * @author Tomasz Pylak
+ */
+public class ImageAnalysisLMCSplitter
+{
+    public static void main(String[] args) throws FileNotFoundException, IOException
+    {
+        CsvReader reader = ScreeningLibraryTransformer.readFile(args[0]);
+        boolean ok = reader.readRecord();
+        assert ok;
+        String[] header = reader.getValues();
+        splitPlates(reader, header);
+    }
+
+    private static void splitPlates(CsvReader reader, String[] header) throws IOException,
+            FileNotFoundException
+    {
+        String prevPlateCode = "";
+        OutputStream out = null;
+        while (reader.readRecord())
+        {
+            String[] row = reader.getValues();
+            String plateCode = row[0];
+            if (plateCode.equals(prevPlateCode) == false)
+            {
+                if (out != null)
+                {
+                    out.close();
+                }
+                System.out.println("Generating " + plateCode);
+                out = new FileOutputStream(new File(plateCode + ".csv"));
+                writeLine(header, out);
+                prevPlateCode = plateCode;
+            }
+            writeLine(row, out);
+        }
+    }
+
+    private static void writeLine(String[] header, OutputStream out) throws IOException
+    {
+        IOUtils.write(join(header) + "\n", out);
+    }
+
+    private static String join(String[] tokens)
+    {
+        for (int i = 0; i < tokens.length; i++)
+        {
+            tokens[i] = tokens[i].replace(';', ',');
+        }
+        return StringUtils.join(tokens, ";");
+    }
+}

screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/transformers/ScreeningLibraryTransformer.java

@@ -60,9 +60,11 @@ public class ScreeningLibraryTransformer
             return;
         }
         String[] headers = csvReader.getValues();
-        IScreeningLibraryColumnExtractor extractor = new QiagenScreeningLibraryColumnExtractor(headers);
+        IScreeningLibraryColumnExtractor extractor =
+                new QiagenScreeningLibraryColumnExtractor(headers);
         LibraryEntityRegistrator registrator =
-                new LibraryEntityRegistrator(extractor, experimentIdentifier, plateGeometry, groupCode);
+                new LibraryEntityRegistrator(extractor, experimentIdentifier, plateGeometry,
+                        groupCode);
         while (csvReader.readRecord())
         {
             String[] row = csvReader.getValues();
@@ -71,14 +73,14 @@ public class ScreeningLibraryTransformer
         System.out.println("Done, look for results in " + new File(".").getAbsolutePath());
     }
 
-    private static CsvReader readFile(String path) throws FileNotFoundException, IOException
+    static CsvReader readFile(String path) throws FileNotFoundException, IOException
     {
-        File masterPlatesFile = new File(path);
-        if (masterPlatesFile.isFile() == false)
+        File file = new File(path);
+        if (file.isFile() == false)
         {
-            error(masterPlatesFile + " does not exist or is not a file.");
+            error(file + " does not exist or is not a file.");
         }
-        FileInputStream fileInputStream = new FileInputStream(masterPlatesFile);
+        FileInputStream fileInputStream = new FileInputStream(file);
 
         CsvReader csvReader = new CsvReader(fileInputStream, Charset.defaultCharset());
         csvReader.setDelimiter(SEPARATOR);