LMS-1300 screening: image analysis reporting plugin

SVN: 13909

screening/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/ImageAnalysisMergedRowsReportingPlugin.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.openbis.dss.generic.server.plugins;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.standard.AbstractDataMergingReportingPlugin;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.DoubleTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.ISerializableComparable;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.IntegerTableCell;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModelRow;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * Reporting plugin that concatenates rows of tabular files of all data sets (stripping the header
+ * lines of all but the first file) and delivers the result back in the table model. Each row has
+ * additional Data Set code column.
+ * 
+ * @author Tomasz Pylak
+ */
+// TODO 2009-12-14, Tomasz Pylak: allow different files to have different headers, merge the same
+// columns and fill columns with empty values if they do not occur in some files.
+public class ImageAnalysisMergedRowsReportingPlugin extends AbstractDataMergingReportingPlugin
+{
+
+    private static final long serialVersionUID = 1L;
+
+    public ImageAnalysisMergedRowsReportingPlugin(Properties properties, File storeRoot)
+    {
+        super(properties, storeRoot, ";");
+    }
+
+    public TableModel createReport(List<DatasetDescription> datasets)
+    {
+        TableModel stringModel = createStringModel(datasets);
+        List<TableModelRow> typedRows = asTypedRows(stringModel.getRows());
+        return new TableModel(stringModel.getHeader(), typedRows);
+    }
+
+    private static List<TableModelRow> asTypedRows(List<TableModelRow> rows)
+    {
+        List<TableModelRow> typedRows = new ArrayList<TableModelRow>();
+        for (TableModelRow row : rows)
+        {
+            typedRows.add(asTypedRow(row));
+        }
+        return typedRows;
+    }
+
+    private static TableModelRow asTypedRow(TableModelRow row)
+    {
+        List<ISerializableComparable> typedValues = new ArrayList<ISerializableComparable>();
+        for (ISerializableComparable value : row.getValues())
+        {
+            typedValues.add(asTypedValue(value));
+        }
+        return new TableModelRow(typedValues);
+    }
+
+    private static ISerializableComparable asTypedValue(ISerializableComparable value)
+    {
+        String text = value.toString();
+        try
+        {
+            Double doubleValue = Double.parseDouble(text);
+            if (doubleValue.intValue() == doubleValue)
+            {
+                return new IntegerTableCell(doubleValue.intValue());
+            } else
+            {
+                return new DoubleTableCell(doubleValue);
+            }
+        } catch (NumberFormatException e)
+        {
+            return value;
+        }
+    }
+
+    // all columns will be strings
+    private TableModel createStringModel(List<DatasetDescription> datasets)
+    {
+        SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
+        builder.addHeader("Data Set Code");
+        if (datasets.isEmpty() == false)
+        {
+            final DatasetDescription firstDataset = datasets.get(0);
+            final String[] titles = getHeaderTitles(firstDataset);
+            for (String title : titles)
+            {
+                builder.addHeader(title);
+            }
+            for (DatasetDescription dataset : datasets)
+            {
+                final File dir = getDataSubDir(dataset);
+                final DatasetFileLines lines = loadFromDirectory(dataset, dir);
+                if (Arrays.equals(titles, lines.getHeaderTokens()) == false)
+                {
+                    throw UserFailureException.fromTemplate(
+                            "All Data Set files should have the same headers, "
+                                    + "but file header of '%s': \n\t '%s' "
+                                    + "is different than file header of '%s': \n\t '%s'.",
+                            firstDataset.getDatasetCode(), StringUtils.join(titles, "\t"), dataset
+                                    .getDatasetCode(), StringUtils.join(lines.getHeaderTokens(),
+                                    "\t"));
+                }
+                addDataRows(builder, dataset, lines.getDataLines());
+            }
+        }
+        return builder.getTableModel();
+    }
+
+}