From 98eea0bbe2ee29c218607f00146a521c1530fa88 Mon Sep 17 00:00:00 2001
From: felmer <felmer>
Date: Tue, 20 Apr 2010 14:46:41 +0000
Subject: [PATCH] SE-236 FeatureStorageProcessor implemented but not tested
SVN: 15537
---
.../dss/genedata/FeatureStorageProcessor.java | 209 ++++++++++++++++++
1 file changed, 209 insertions(+)
create mode 100644 screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/FeatureStorageProcessor.java
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/FeatureStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/FeatureStorageProcessor.java
new file mode 100644
index 00000000000..2b3442fbaed
--- /dev/null
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/genedata/FeatureStorageProcessor.java
@@ -0,0 +1,209 @@
+/*
+ * 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.dss.genedata;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+import java.util.Properties;
+import java.util.StringTokenizer;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.etlserver.DefaultStorageProcessor;
+import ch.systemsx.cisd.etlserver.utils.Column;
+import ch.systemsx.cisd.etlserver.utils.TableBuilder;
+
+/**
+ *
+ *
+ * @author Franz-Josef Elmer
+ */
+public class FeatureStorageProcessor extends DefaultStorageProcessor
+{
+ private static final char DELIMITER = ',';
+ private static final String LAYER_PREFIX = "<Layer=";
+ private File originalFile;
+
+ private final class ColumnsBuilder
+ {
+ private final List<Column> columns = new ArrayList<Column>();
+ private final List<String> rowLetters = new ArrayList<String>();
+ private TableBuilder tableBuilder;
+ private int numberOfColumns;
+
+ public void startNewColumn(String columnName)
+ {
+ if (tableBuilder != null)
+ {
+ columns.addAll(tableBuilder.getColumns());
+ }
+ tableBuilder = new TableBuilder(columnName);
+
+ }
+
+ public void checkColumnsLine(int lineIndex, String line)
+ {
+ int columnCount = new StringTokenizer(line).countTokens();
+ if (numberOfColumns == 0)
+ {
+ numberOfColumns = columnCount;
+ }
+ if (numberOfColumns != columnCount)
+ {
+ throw error(lineIndex, line, "Inconsistent number of columns: Expected "
+ + numberOfColumns + " but was " + columnCount);
+ }
+
+ }
+
+ public void addRow(int lineIndex, String line)
+ {
+ StringTokenizer tokenizer = new StringTokenizer(line);
+ int countTokens = tokenizer.countTokens();
+ if (countTokens != numberOfColumns + 1)
+ {
+ throw error(lineIndex, line, "Inconsistent number of columns: Expected "
+ + numberOfColumns + " but was " + (countTokens - 1));
+ }
+ String rowLetter = tokenizer.nextToken();
+ if (rowLetters.contains(rowLetter) == false)
+ {
+ rowLetters.add(rowLetter);
+ }
+ while (tokenizer.hasMoreTokens())
+ {
+ if (tableBuilder != null)
+ {
+ tableBuilder.addRow(tokenizer.nextToken());
+ }
+ }
+ }
+
+ public int getNumberOfWells()
+ {
+ return numberOfColumns * rowLetters.size();
+ }
+
+ public String getRowLetter(int index)
+ {
+ return rowLetters.get(index % rowLetters.size());
+ }
+
+ public int getColumnNumber(int index)
+ {
+ return index % numberOfColumns + 1;
+ }
+
+ public List<Column> getColumns()
+ {
+ return columns;
+ }
+ }
+
+ public FeatureStorageProcessor(Properties properties)
+ {
+ super(properties);
+ }
+
+ @Override
+ protected void transform(File originalDataSet, File targetFolderForTransformedDataSet)
+ {
+ originalFile = originalDataSet;
+ List<String> lines = FileUtilities.loadToStringList(originalDataSet);
+ if (lines.isEmpty())
+ {
+ throw new UserFailureException("Empty file: " + originalDataSet.getName());
+ }
+ String barCode = extractBarCode(lines.get(0));
+ ColumnsBuilder columnsBuilder = new ColumnsBuilder();
+ for (int i = 1; i < lines.size(); i++)
+ {
+ String line = lines.get(i).trim();
+ if (line.length() == 0)
+ {
+ continue;
+ }
+ if (line.startsWith(LAYER_PREFIX))
+ {
+ columnsBuilder.startNewColumn(extractLayer(line, i));
+ } else if (line.startsWith("1"))
+ {
+ columnsBuilder.checkColumnsLine(i, line);
+ } else
+ {
+ columnsBuilder.addRow(i, line);
+ }
+ }
+ List<Column> columns = columnsBuilder.getColumns();
+ StringBuilder builder = new StringBuilder();
+ builder.append("barcode").append(DELIMITER).append("row").append(DELIMITER).append("col");
+ for (Column column : columns)
+ {
+ builder.append(DELIMITER).append(column.getHeader());
+ }
+ for (int i = 0, n = columnsBuilder.getNumberOfWells(); i < n; i++)
+ {
+ builder.append('\n').append(barCode);
+ builder.append(DELIMITER).append(columnsBuilder.getRowLetter(i));
+ builder.append(DELIMITER).append(columnsBuilder.getColumnNumber(i));
+ for (Column column : columns)
+ {
+ builder.append(DELIMITER).append(column.getValues().get(i));
+ }
+ }
+ File originalDirectory = getOriginalDirectory(targetFolderForTransformedDataSet);
+ File file = new File(originalDirectory, originalDataSet.getName() + ".txt");
+ FileUtilities.writeToFile(file, builder.toString());
+ }
+
+ @Override
+ public void commit()
+ {
+ if (originalFile != null && originalFile.exists())
+ {
+ originalFile.delete();
+ }
+ }
+
+ private String extractBarCode(String firstLine)
+ {
+ int indexOfEqual = firstLine.indexOf('=');
+ if (indexOfEqual < 0)
+ {
+ throw error(0, firstLine, "Missing '='");
+ }
+ return firstLine.substring(indexOfEqual + 1).trim();
+ }
+
+ private String extractLayer(String line, int lineIndex)
+ {
+ String layer = line.substring(LAYER_PREFIX.length());
+ if (layer.endsWith(">") == false)
+ {
+ throw error(lineIndex, line, "Missing '>' at the end");
+ }
+ return layer.substring(0, layer.length() - 1);
+ }
+
+ private UserFailureException error(int lineIndex, String line, String reason)
+ {
+ return new UserFailureException("Error in line " + lineIndex + 1
+ + ": " + reason + ": " + line);
+ }
+
+}
--
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