From b21ad7fee7804b19a131d9846b62518a6d465631 Mon Sep 17 00:00:00 2001
From: brinn <brinn>
Date: Fri, 11 Sep 2009 18:34:48 +0000
Subject: [PATCH] add: MergedColumnDataReportingPlugin for column-based merging
of TSV files change: rename MergedDataReportingPlugin ->
MergedRowDataReportingPlugin
SVN: 12557
---
.../AbstractDataMergingReportingPlugin.java | 197 +++++++++++++
.../DatasetModificationReportingPlugin.java | 4 +-
.../plugins/demo/DemoReportingPlugin.java | 10 +-
.../demo/MergedColumnDataReportingPlugin.java | 60 ++++
.../demo/MergedDataReportingPlugin.java | 264 ------------------
.../demo/MergedRowDataReportingPlugin.java | 83 ++++++
.../plugins/tasks/DatasetFileLines.java | 88 ++++++
.../tasks/IterativeTableModelBuilder.java | 144 ++++++++++
...lder.java => SimpleTableModelBuilder.java} | 4 +-
.../tasks/IterativeTableModelBuilderTest.java | 264 ++++++++++++++++++
10 files changed, 845 insertions(+), 273 deletions(-)
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/AbstractDataMergingReportingPlugin.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedColumnDataReportingPlugin.java
delete mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedDataReportingPlugin.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedRowDataReportingPlugin.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/DatasetFileLines.java
create mode 100644 datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IterativeTableModelBuilder.java
rename datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/{TableModelBuilder.java => SimpleTableModelBuilder.java} (96%)
create mode 100644 datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IterativeTableModelBuilderTest.java
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/AbstractDataMergingReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/AbstractDataMergingReportingPlugin.java
new file mode 100644
index 00000000000..0f2f56b43af
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/AbstractDataMergingReportingPlugin.java
@@ -0,0 +1,197 @@
+/*
+ * 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.demo;
+
+import java.io.File;
+import java.io.FileReader;
+import java.io.IOException;
+import java.io.Reader;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+import java.util.Properties;
+
+import org.apache.commons.io.IOUtils;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.filesystem.FileUtilities;
+import ch.systemsx.cisd.common.parser.ParserException;
+import ch.systemsx.cisd.common.parser.ParsingException;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * Common super class of all tsv-based data merging reporting plugins.
+ *
+ * @author Bernd Rinn
+ */
+public abstract class AbstractDataMergingReportingPlugin extends AbstractDatastorePlugin implements
+ IReportingPluginTask
+{
+ private static final String FILE_INCLUDE_PATTERN = "file-include-pattern";
+
+ private static final String FILE_EXCLUDE_PATTERN = "file-exclude-pattern";
+
+ /** pattern for files that should be excluded (e.g. data set properties files) */
+ public final static String DEFAULT_EXCLUDED_FILE_NAMES_PATTERN = ".*\\.tsv";
+
+ private final String excludePattern;
+
+ private final String includePatternOrNull;
+
+ protected AbstractDataMergingReportingPlugin(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ final String excludePatternOrNull = properties.getProperty(FILE_EXCLUDE_PATTERN);
+ if (excludePatternOrNull == null)
+ {
+ this.excludePattern = DEFAULT_EXCLUDED_FILE_NAMES_PATTERN;
+ } else
+ {
+ this.excludePattern = excludePatternOrNull;
+ }
+ this.includePatternOrNull = properties.getProperty(FILE_INCLUDE_PATTERN);
+ }
+
+ protected String[] getHeaderTitles(DatasetDescription dataset)
+ {
+ File dir = getOriginalDir(dataset);
+ final DatasetFileLines lines = loadFromDirectory(dataset, dir);
+ return lines.getHeaderTokens();
+ }
+
+ protected static void addDataRows(SimpleTableModelBuilder builder, DatasetDescription dataset,
+ List<String[]> dataLines)
+ {
+ String datasetCode = dataset.getDatasetCode();
+ for (String[] dataTokens : dataLines)
+ {
+ addDataRow(builder, datasetCode, dataTokens);
+ }
+ }
+
+ protected static void addDataRow(SimpleTableModelBuilder builder, String datasetCode,
+ String[] dataTokens)
+ {
+ List<String> row = new ArrayList<String>();
+ row.add(datasetCode);
+ row.addAll(Arrays.asList(dataTokens));
+ builder.addRow(row);
+ }
+
+ /**
+ * Loads {@link DatasetFileLines} from the file found in the specified directory.
+ *
+ * @throws IOExceptionUnchecked if a {@link IOException} has occurred.
+ */
+ protected DatasetFileLines loadFromDirectory(DatasetDescription dataset, final File dir)
+ throws ParserException, ParsingException, IllegalArgumentException,
+ IOExceptionUnchecked
+ {
+ assert dir != null : "Given file must not be null";
+ assert dir.isDirectory() : "Given file '" + dir.getAbsolutePath() + "' is not a directory.";
+
+ File[] datasetFiles = FileUtilities.listFiles(dir);
+ List<File> datasetFilesToMerge = new ArrayList<File>();
+ for (File datasetFile : datasetFiles)
+ {
+ if (datasetFile.isDirectory())
+ {
+ // recursively go down the directories
+ return loadFromDirectory(dataset, datasetFile);
+ } else
+ {
+ // exclude files with properties
+ if (isFileExcluded(datasetFile) == false)
+ {
+ datasetFilesToMerge.add(datasetFile);
+ }
+ }
+
+ }
+ if (datasetFilesToMerge.size() != 1)
+ {
+ throw UserFailureException
+ .fromTemplate(
+ "Directory with Data Set '%s' data ('%s') should contain exactly 1 file with data but %s files were found.",
+ dataset.getDatasetCode(), dir.getAbsolutePath(), datasetFilesToMerge
+ .size());
+ } else
+ {
+ return loadFromFile(dataset, datasetFilesToMerge.get(0));
+ }
+ }
+
+ /**
+ * Loads {@link DatasetFileLines} from the specified tab file.
+ *
+ * @throws IOExceptionUnchecked if a {@link IOException} has occurred.
+ */
+ protected DatasetFileLines loadFromFile(DatasetDescription dataset, final File file)
+ throws ParserException, ParsingException, IllegalArgumentException,
+ IOExceptionUnchecked
+ {
+ assert file != null : "Given file must not be null";
+ assert file.isFile() : "Given file '" + file.getAbsolutePath() + "' is not a file.";
+
+ FileReader reader = null;
+ try
+ {
+ reader = new FileReader(file);
+ return load(dataset, reader, file);
+ } catch (final IOException ex)
+ {
+ throw new IOExceptionUnchecked(ex);
+ } finally
+ {
+ IOUtils.closeQuietly(reader);
+ }
+ }
+
+ /**
+ * Loads data from the specified reader.
+ *
+ * @throws IOException
+ */
+ @SuppressWarnings("unchecked")
+ protected DatasetFileLines load(final DatasetDescription dataset, final Reader reader,
+ final File file) throws ParserException, ParsingException, IllegalArgumentException,
+ IOException
+ {
+ assert reader != null : "Unspecified reader";
+
+ final List<String> lines = IOUtils.readLines(reader);
+ return new DatasetFileLines(file, dataset, lines);
+ }
+
+ protected boolean isFileExcluded(File file)
+ {
+ if (includePatternOrNull != null)
+ {
+ return file.getName().matches(includePatternOrNull) == false;
+ } else
+ {
+ return file.getName().matches(excludePattern);
+ }
+ }
+
+ private static final long serialVersionUID = 1L;
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DatasetModificationReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DatasetModificationReportingPlugin.java
index 791a69545ec..d3e4b579d5a 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DatasetModificationReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DatasetModificationReportingPlugin.java
@@ -23,7 +23,7 @@ import java.util.List;
import java.util.Properties;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.TableModelBuilder;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel.TableModelColumnType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
@@ -46,7 +46,7 @@ public class DatasetModificationReportingPlugin extends AbstractDatastorePlugin
public TableModel createReport(List<DatasetDescription> datasets)
{
- TableModelBuilder builder = new TableModelBuilder();
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
builder.addHeader("File", TableModelColumnType.TEXT);
builder.addHeader("Modification date", TableModelColumnType.DATE);
for (DatasetDescription dataset : datasets)
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
index 2711dc5f4ac..135f9c9bc9e 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/DemoReportingPlugin.java
@@ -25,7 +25,7 @@ import org.apache.commons.io.FileUtils;
import ch.systemsx.cisd.common.filesystem.FileUtilities;
import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.TableModelBuilder;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel.TableModelColumnType;
import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
@@ -46,7 +46,7 @@ public class DemoReportingPlugin extends AbstractDatastorePlugin implements IRep
public TableModel createReport(List<DatasetDescription> datasets)
{
- TableModelBuilder builder = new TableModelBuilder();
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
builder.addHeader("Dataset code", TableModelColumnType.TEXT);
builder.addHeader("Name", TableModelColumnType.TEXT);
builder.addHeader("Size", TableModelColumnType.INTEGER);
@@ -64,7 +64,7 @@ public class DemoReportingPlugin extends AbstractDatastorePlugin implements IRep
return builder.getTableModel();
}
- private static void describe(TableModelBuilder builder, DatasetDescription dataset, File file)
+ private static void describe(SimpleTableModelBuilder builder, DatasetDescription dataset, File file)
{
if (file.isFile())
{
@@ -79,14 +79,14 @@ public class DemoReportingPlugin extends AbstractDatastorePlugin implements IRep
}
}
- private void describeUnknown(TableModelBuilder builder, DatasetDescription dataset, File file)
+ private void describeUnknown(SimpleTableModelBuilder builder, DatasetDescription dataset, File file)
{
String datasetCode = dataset.getDatasetCode();
List<String> row = Arrays.asList(datasetCode, file.getName(), "[does not exist]");
builder.addRow(row);
}
- private static void describeFile(TableModelBuilder builder, DatasetDescription dataset,
+ private static void describeFile(SimpleTableModelBuilder builder, DatasetDescription dataset,
File file)
{
List<String> row =
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedColumnDataReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedColumnDataReportingPlugin.java
new file mode 100644
index 00000000000..18afb09dc58
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedColumnDataReportingPlugin.java
@@ -0,0 +1,60 @@
+/*
+ * 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.demo;
+
+import java.io.File;
+import java.util.List;
+import java.util.Properties;
+
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IterativeTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * Reporting plugin that concatenates column tabular files of all data sets, using a
+ * <code>mergeColumn</code> to identify matching rows.
+ *
+ * @author Bernd Rinn
+ */
+public class MergedColumnDataReportingPlugin extends AbstractDataMergingReportingPlugin
+{
+ private static final long serialVersionUID = 1L;
+
+ private static final String ROW_ID_COLUMN_HEADER = "row-id-column-header";
+
+ private final String rowIdentifierColumnHeader;
+
+ public MergedColumnDataReportingPlugin(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ rowIdentifierColumnHeader = properties.getProperty(ROW_ID_COLUMN_HEADER);
+ }
+
+ public TableModel createReport(List<DatasetDescription> datasets)
+ {
+ final IterativeTableModelBuilder builder =
+ new IterativeTableModelBuilder(rowIdentifierColumnHeader);
+ for (DatasetDescription dataset : datasets)
+ {
+ final DatasetFileLines lines = loadFromDirectory(dataset, getOriginalDir(dataset));
+ builder.addFile(lines);
+ }
+ return builder.getTableModel();
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedDataReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedDataReportingPlugin.java
deleted file mode 100644
index 803c56c41a0..00000000000
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedDataReportingPlugin.java
+++ /dev/null
@@ -1,264 +0,0 @@
-/*
- * 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.demo;
-
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.Reader;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-import java.util.Properties;
-
-import org.apache.commons.io.IOUtils;
-import org.apache.commons.lang.StringUtils;
-
-import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
-import ch.systemsx.cisd.common.exceptions.UserFailureException;
-import ch.systemsx.cisd.common.filesystem.FileUtilities;
-import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.common.parser.ParsingException;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.IReportingPluginTask;
-import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.TableModelBuilder;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
-import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel.TableModelColumnType;
-import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
-
-/**
- * Reporting plugin that concatenates 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 Piotr Buczek
- */
-public class MergedDataReportingPlugin extends AbstractDatastorePlugin implements
- IReportingPluginTask
-{
-
- private static final long serialVersionUID = 1L;
- /** pattern for files that should be excluded (e.g. data set properties files) */
- public final static String EXCLUDED_FILE_NAMES_PATTERN = ".*\\.tsv";
-
- public MergedDataReportingPlugin(Properties properties, File storeRoot)
- {
- super(properties, storeRoot);
- }
-
- public TableModel createReport(List<DatasetDescription> datasets)
- {
- TableModelBuilder builder = new TableModelBuilder();
- builder.addHeader("Data Set Code", TableModelColumnType.TEXT);
- if (datasets.isEmpty() == false)
- {
- final DatasetDescription firstDataset = datasets.get(0);
- final String[] titles = getHeaderTitles(firstDataset);
- for (String title : titles)
- {
- builder.addHeader(title, TableModelColumnType.TEXT);
- }
- for (DatasetDescription dataset : datasets)
- {
- final File dir = getOriginalDir(dataset);
- final DatasetFileLines lines = SimpleTabFileLoader.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();
- }
-
- private String[] getHeaderTitles(DatasetDescription dataset)
- {
- File dir = getOriginalDir(dataset);
- DatasetFileLines lines = SimpleTabFileLoader.loadFromDirectory(dataset, dir);
- return lines.getHeaderTokens();
- }
-
- private static void addDataRows(TableModelBuilder builder, DatasetDescription dataset,
- List<String[]> dataLines)
- {
- String datasetCode = dataset.getDatasetCode();
- for (String[] dataTokens : dataLines)
- {
- addDataRow(builder, datasetCode, dataTokens);
- }
- }
-
- private static void addDataRow(TableModelBuilder builder, String datasetCode,
- String[] dataTokens)
- {
- List<String> row = new ArrayList<String>();
- row.add(datasetCode);
- row.addAll(Arrays.asList(dataTokens));
- builder.addRow(row);
- }
-
- private static class SimpleTabFileLoader
- {
- /**
- * Loads {@link DatasetFileLines} from the file found in the specified directory.
- *
- * @throws IOExceptionUnchecked if a {@link IOException} has occurred.
- */
- private static DatasetFileLines loadFromDirectory(DatasetDescription dataset, final File dir)
- throws ParserException, ParsingException, IllegalArgumentException,
- IOExceptionUnchecked
- {
- assert dir != null : "Given file must not be null";
- assert dir.isDirectory() : "Given file '" + dir.getAbsolutePath()
- + "' is not a directory.";
-
- File[] datasetFiles = FileUtilities.listFiles(dir);
- List<File> datasetFilesToMerge = new ArrayList<File>();
- for (File datasetFile : datasetFiles)
- {
- if (datasetFile.isDirectory())
- {
- // recursively go down the directories
- return loadFromDirectory(dataset, datasetFile);
- } else
- {
- // exclude files with properties
- if (isFileExcluded(datasetFile) == false)
- {
- datasetFilesToMerge.add(datasetFile);
- }
- }
-
- }
- if (datasetFilesToMerge.size() != 1)
- {
- throw UserFailureException
- .fromTemplate(
- "Directory with Data Set '%s' data ('%s') should contain exactly 1 file with data but %s files were found.",
- dataset.getDatasetCode(), dir.getAbsolutePath(),
- datasetFilesToMerge.size());
- } else
- {
- return loadFromFile(dataset, datasetFilesToMerge.get(0));
- }
- }
-
- private static boolean isFileExcluded(File file)
- {
- return file.getName().matches(EXCLUDED_FILE_NAMES_PATTERN);
- }
-
- /**
- * Loads {@link DatasetFileLines} from the specified tab file.
- *
- * @throws IOExceptionUnchecked if a {@link IOException} has occurred.
- */
- private static DatasetFileLines loadFromFile(DatasetDescription dataset, final File file)
- throws ParserException, ParsingException, IllegalArgumentException,
- IOExceptionUnchecked
- {
- assert file != null : "Given file must not be null";
- assert file.isFile() : "Given file '" + file.getAbsolutePath() + "' is not a file.";
-
- FileReader reader = null;
- try
- {
- reader = new FileReader(file);
- return load(dataset, reader);
- } catch (final IOException ex)
- {
- throw new IOExceptionUnchecked(ex);
- } finally
- {
- IOUtils.closeQuietly(reader);
- }
- }
-
- /**
- * Loads data from the specified reader.
- *
- * @throws IOException
- */
- @SuppressWarnings("unchecked")
- private static DatasetFileLines load(DatasetDescription dataset, final Reader reader)
- throws ParserException, ParsingException, IllegalArgumentException, IOException
- {
- assert reader != null : "Unspecified reader";
-
- final List<String> lines = IOUtils.readLines(reader);
- return new DatasetFileLines(dataset, lines);
- }
- }
-
- private static class DatasetFileLines
- {
- private final String[] headerTokens;
-
- private final List<String[]> dataLines;
-
- public DatasetFileLines(DatasetDescription dataset, List<String> lines)
- {
- super();
- if (lines.size() < 2)
- {
- throw UserFailureException.fromTemplate(
- "Data Set '%s' file should have at least 2 lines instead of %s.", dataset
- .getDatasetCode(), lines.size());
- }
- this.headerTokens = parseLine(lines.get(0));
- dataLines = new ArrayList<String[]>(lines.size());
- for (int i = 1; i < lines.size(); i++)
- {
- String[] dataTokens = parseLine(lines.get(i));
- if (headerTokens.length != dataTokens.length)
- {
- throw UserFailureException.fromTemplate(
- "Number of columns in header (%s) does not match number of columns "
- + "in %d data row (%s) in Data Set '%s' file.",
- headerTokens.length, i, dataTokens.length, dataset.getDatasetCode());
- }
- dataLines.add(dataTokens);
- }
- }
-
- /** splits line with '\t' and strips quotes from every token */
- private String[] parseLine(String line)
- {
- String[] tokens = line.split("\t");
- return StringUtils.stripAll(tokens, "'\"");
- }
-
- public String[] getHeaderTokens()
- {
- return headerTokens;
- }
-
- public List<String[]> getDataLines()
- {
- return dataLines;
- }
-
- }
-
-}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedRowDataReportingPlugin.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedRowDataReportingPlugin.java
new file mode 100644
index 00000000000..5e3c9ca1494
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/demo/MergedRowDataReportingPlugin.java
@@ -0,0 +1,83 @@
+/*
+ * 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.demo;
+
+import java.io.File;
+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.tasks.DatasetFileLines;
+import ch.systemsx.cisd.openbis.dss.generic.server.plugins.tasks.SimpleTableModelBuilder;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel.TableModelColumnType;
+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 Piotr Buczek
+ */
+public class MergedRowDataReportingPlugin extends AbstractDataMergingReportingPlugin
+{
+
+ private static final long serialVersionUID = 1L;
+
+ public MergedRowDataReportingPlugin(Properties properties, File storeRoot)
+ {
+ super(properties, storeRoot);
+ }
+
+ public TableModel createReport(List<DatasetDescription> datasets)
+ {
+ SimpleTableModelBuilder builder = new SimpleTableModelBuilder();
+ builder.addHeader("Data Set Code", TableModelColumnType.TEXT);
+ if (datasets.isEmpty() == false)
+ {
+ final DatasetDescription firstDataset = datasets.get(0);
+ final String[] titles = getHeaderTitles(firstDataset);
+ for (String title : titles)
+ {
+ builder.addHeader(title, TableModelColumnType.TEXT);
+ }
+ for (DatasetDescription dataset : datasets)
+ {
+ final File dir = getOriginalDir(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();
+ }
+
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/DatasetFileLines.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/DatasetFileLines.java
new file mode 100644
index 00000000000..35c045c178a
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/DatasetFileLines.java
@@ -0,0 +1,88 @@
+/*
+ * 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.tasks;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.lang.StringUtils;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * Stores the lines of a tsv file.
+ *
+ * @author Bernd Rinn
+ */
+public class DatasetFileLines
+{
+ private final String[] headerTokens;
+
+ private final List<String[]> dataLines;
+
+ private final File file;
+
+ public DatasetFileLines(File file, DatasetDescription dataset, List<String> lines)
+ {
+ this.file = file;
+ if (lines.size() < 2)
+ {
+ throw UserFailureException.fromTemplate(
+ "Data Set '%s' file should have at least 2 lines instead of %s.", dataset
+ .getDatasetCode(), lines.size());
+ }
+ this.headerTokens = parseLine(lines.get(0));
+ dataLines = new ArrayList<String[]>(lines.size());
+ for (int i = 1; i < lines.size(); i++)
+ {
+ String[] dataTokens = parseLine(lines.get(i));
+ if (headerTokens.length != dataTokens.length)
+ {
+ throw UserFailureException.fromTemplate(
+ "Number of columns in header (%s) does not match number of columns "
+ + "in %d data row (%s) in Data Set '%s' file.",
+ headerTokens.length, i, dataTokens.length, dataset.getDatasetCode());
+ }
+ dataLines.add(dataTokens);
+ }
+ }
+
+ /** splits line with '\t' and strips quotes from every token */
+ private String[] parseLine(String line)
+ {
+ String[] tokens = line.split("\t");
+ return StringUtils.stripAll(tokens, "'\"");
+ }
+
+ public final File getFile()
+ {
+ return file;
+ }
+
+ public String[] getHeaderTokens()
+ {
+ return headerTokens;
+ }
+
+ public List<String[]> getDataLines()
+ {
+ return dataLines;
+ }
+
+}
\ No newline at end of file
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IterativeTableModelBuilder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IterativeTableModelBuilder.java
new file mode 100644
index 00000000000..044ce6d900e
--- /dev/null
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IterativeTableModelBuilder.java
@@ -0,0 +1,144 @@
+/*
+ * 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.tasks;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.LinkedHashMap;
+import java.util.LinkedHashSet;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.Map.Entry;
+
+import org.apache.log4j.Logger;
+
+import ch.systemsx.cisd.common.logging.LogCategory;
+import ch.systemsx.cisd.common.logging.LogFactory;
+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.basic.dto.TableModel.TableModelColumnHeader;
+import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel.TableModelColumnType;
+
+/**
+ * A table model builder that can take new columns and rows iteratively.
+ *
+ * @author Bernd Rinn
+ */
+public class IterativeTableModelBuilder
+{
+ private final static Logger operationLog =
+ LogFactory.getLogger(LogCategory.OPERATION, IterativeTableModelBuilderTest.class);
+
+ private final String rowIdentifierColumnHeader;
+
+ /** Set of row identifiers. */
+ private final Set<String> rowIdentifiers = new LinkedHashSet<String>();
+
+ /** Map from column name to the map that maps row identifier to value. */
+ private final Map<String, Map<String, String>> columnMap =
+ new LinkedHashMap<String, Map<String, String>>();
+
+ public IterativeTableModelBuilder(String rowIdentifierColumnHeader)
+ {
+ this.rowIdentifierColumnHeader = rowIdentifierColumnHeader;
+ }
+
+ private int findIndexOfIdentifierColumn(DatasetFileLines lines)
+ {
+ int idx = 0;
+ for (String columnHeader : lines.getHeaderTokens())
+ {
+ if (rowIdentifierColumnHeader.equals(columnHeader))
+ {
+ return idx;
+ }
+ ++idx;
+ }
+ return -1;
+ }
+
+ public void addFile(DatasetFileLines lines)
+ {
+ final int colIndexOfRowId = findIndexOfIdentifierColumn(lines);
+ if (colIndexOfRowId < 0)
+ {
+ operationLog.warn("Skip file '" + lines.getFile().getPath() + "' as it has no column '"
+ + rowIdentifierColumnHeader + "'.");
+ return;
+ }
+ final String[] columnHeaders = lines.getHeaderTokens();
+ int colIdx = 0;
+ for (String columnHeader : columnHeaders)
+ {
+ // Does a column with that name already exist?
+ Map<String, String> column = columnMap.get(columnHeader);
+ if (column != null && colIdx == colIndexOfRowId)
+ {
+ addLineToColumn(lines, column, colIdx, colIndexOfRowId);
+ ++colIdx;
+ continue;
+ }
+ if (column != null)
+ {
+ columnHeader += "X";
+ }
+ column = new HashMap<String, String>();
+ columnMap.put(columnHeader, column);
+ addLineToColumn(lines, column, colIdx, colIndexOfRowId);
+ ++colIdx;
+ }
+ }
+
+ private void addLineToColumn(DatasetFileLines lines, Map<String, String> column, int colIdx,
+ final int colIndexOfRowId)
+ {
+ for (String[] line : lines.getDataLines())
+ {
+ final String rowId = line[colIndexOfRowId];
+ rowIdentifiers.add(rowId);
+ column.put(rowId, line[colIdx]);
+ }
+ }
+
+ /**
+ * Returns the table model that was built iteratively.
+ */
+ public TableModel getTableModel()
+ {
+ final List<TableModelColumnHeader> headers =
+ new ArrayList<TableModelColumnHeader>(columnMap.size());
+ final List<TableModelRow> rows = new ArrayList<TableModelRow>(rowIdentifiers.size());
+ int idx = 0;
+ for (Entry<String, Map<String, String>> column : columnMap.entrySet())
+ {
+ headers.add(new TableModelColumnHeader(column.getKey(), TableModelColumnType.TEXT,
+ idx++));
+ }
+ for (String rowId : rowIdentifiers)
+ {
+ final List<String> rowValues = new ArrayList<String>(headers.size());
+ for (TableModelColumnHeader header : headers)
+ {
+ final String valueOrNull = columnMap.get(header.getTitle()).get(rowId);
+ rowValues.add((valueOrNull == null) ? "" : valueOrNull);
+ }
+ rows.add(new TableModelRow(rowValues));
+ }
+ return new TableModel(headers, rows);
+ }
+}
diff --git a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/TableModelBuilder.java b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/SimpleTableModelBuilder.java
similarity index 96%
rename from datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/TableModelBuilder.java
rename to datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/SimpleTableModelBuilder.java
index 237d9e901c4..31b6cd462c0 100644
--- a/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/TableModelBuilder.java
+++ b/datastore_server/source/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/SimpleTableModelBuilder.java
@@ -29,13 +29,13 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.TableModel.TableModelCo
*
* @author Tomasz Pylak
*/
-public class TableModelBuilder
+public class SimpleTableModelBuilder
{
private List<TableModelRow> rows;
private List<TableModelColumnHeader> header;
- public TableModelBuilder()
+ public SimpleTableModelBuilder()
{
this.rows = new ArrayList<TableModelRow>();
this.header = new ArrayList<TableModelColumnHeader>();
diff --git a/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IterativeTableModelBuilderTest.java b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IterativeTableModelBuilderTest.java
new file mode 100644
index 00000000000..7d8ea1de2f6
--- /dev/null
+++ b/datastore_server/sourceTest/java/ch/systemsx/cisd/openbis/dss/generic/server/plugins/tasks/IterativeTableModelBuilderTest.java
@@ -0,0 +1,264 @@
+/*
+ * 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.tasks;
+
+import static org.testng.AssertJUnit.*;
+
+import java.io.File;
+import java.util.Arrays;
+import java.util.List;
+
+import org.testng.annotations.BeforeTest;
+import org.testng.annotations.Test;
+
+import ch.systemsx.cisd.common.logging.LogInitializer;
+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.basic.dto.TableModel.TableModelColumnHeader;
+import ch.systemsx.cisd.openbis.generic.shared.dto.DatasetDescription;
+
+/**
+ * Test cases for the {@link IterativeTableModelBuilder}.
+ *
+ * @author Bernd Rinn
+ */
+public class IterativeTableModelBuilderTest
+{
+ @BeforeTest
+ public void setUp()
+ {
+ LogInitializer.init();
+ }
+
+ @Test
+ public void testHappyCaseOneFile()
+ {
+ final IterativeTableModelBuilder builder = new IterativeTableModelBuilder("id");
+ final DatasetDescription description =
+ new DatasetDescription("code", "location", "sampleCode", "groupCode");
+ final DatasetFileLines lines =
+ new DatasetFileLines(new File("doesn't matter"), description, Arrays.asList(
+ "id\tval", "a\tA", "b\tB", "c\tC"));
+ builder.addFile(lines);
+ final TableModel model = builder.getTableModel();
+ final List<TableModelColumnHeader> headers = model.getHeader();
+ assertEquals(2, headers.size());
+ assertEquals("id", headers.get(0).getTitle());
+ assertEquals(0, headers.get(0).getIndex());
+ assertEquals("val", headers.get(1).getTitle());
+ assertEquals(1, headers.get(1).getIndex());
+ final List<TableModelRow> rows = model.getRows();
+ assertEquals(3, rows.size());
+ final List<String> row0 = rows.get(0).getValues();
+ assertEquals(2, row0.size());
+ assertEquals("a", row0.get(0));
+ assertEquals("A", row0.get(1));
+ final List<String> row1 = rows.get(1).getValues();
+ assertEquals(2, row1.size());
+ assertEquals("b", row1.get(0));
+ assertEquals("B", row1.get(1));
+ final List<String> row2 = rows.get(2).getValues();
+ assertEquals(2, row2.size());
+ assertEquals("c", row2.get(0));
+ assertEquals("C", row2.get(1));
+ }
+
+ @Test
+ public void testHappyCaseTwoFiles()
+ {
+ final IterativeTableModelBuilder builder = new IterativeTableModelBuilder("id");
+ final DatasetDescription description =
+ new DatasetDescription("code", "location", "sampleCode", "groupCode");
+ final DatasetFileLines lines =
+ new DatasetFileLines(new File("doesn't matter"), description, Arrays.asList(
+ "id\tval", "a\tA", "b\tB", "c\tC"));
+ builder.addFile(lines);
+ final DatasetFileLines lines2 =
+ new DatasetFileLines(new File("doesn't matter"), description, Arrays.asList(
+ "id\tval2", "a\tD", "b\tE", "c\tF"));
+ builder.addFile(lines2);
+ final TableModel model = builder.getTableModel();
+ final List<TableModelColumnHeader> headers = model.getHeader();
+ assertEquals(3, headers.size());
+ assertEquals("id", headers.get(0).getTitle());
+ assertEquals(0, headers.get(0).getIndex());
+ assertEquals("val", headers.get(1).getTitle());
+ assertEquals(1, headers.get(1).getIndex());
+ assertEquals("val2", headers.get(2).getTitle());
+ assertEquals(2, headers.get(2).getIndex());
+ final List<TableModelRow> rows = model.getRows();
+ assertEquals(3, rows.size());
+ final List<String> row0 = rows.get(0).getValues();
+ assertEquals(3, row0.size());
+ assertEquals("a", row0.get(0));
+ assertEquals("A", row0.get(1));
+ assertEquals("D", row0.get(2));
+ final List<String> row1 = rows.get(1).getValues();
+ assertEquals(3, row1.size());
+ assertEquals("b", row1.get(0));
+ assertEquals("B", row1.get(1));
+ assertEquals("E", row1.get(2));
+ final List<String> row2 = rows.get(2).getValues();
+ assertEquals(3, row2.size());
+ assertEquals("c", row2.get(0));
+ assertEquals("C", row2.get(1));
+ assertEquals("F", row2.get(2));
+ }
+
+ @Test
+ public void testHappyCaseTwoFilesDifferentIds()
+ {
+ final IterativeTableModelBuilder builder = new IterativeTableModelBuilder("id");
+ final DatasetDescription description =
+ new DatasetDescription("code", "location", "sampleCode", "groupCode");
+ final DatasetFileLines lines =
+ new DatasetFileLines(new File("doesn't matter"), description, Arrays.asList(
+ "id\tval", "a\tA", "b\tB", "c\tC"));
+ builder.addFile(lines);
+ final DatasetFileLines lines2 =
+ new DatasetFileLines(new File("doesn't matter"), description, Arrays.asList(
+ "id\tval2", "d\tD", "b\tE", "f\tF"));
+ builder.addFile(lines2);
+ final TableModel model = builder.getTableModel();
+ final List<TableModelColumnHeader> headers = model.getHeader();
+ assertEquals(3, headers.size());
+ assertEquals("id", headers.get(0).getTitle());
+ assertEquals(0, headers.get(0).getIndex());
+ assertEquals("val", headers.get(1).getTitle());
+ assertEquals(1, headers.get(1).getIndex());
+ assertEquals("val2", headers.get(2).getTitle());
+ assertEquals(2, headers.get(2).getIndex());
+ final List<TableModelRow> rows = model.getRows();
+ assertEquals(5, rows.size());
+ final List<String> row0 = rows.get(0).getValues();
+ assertEquals(3, row0.size());
+ assertEquals("a", row0.get(0));
+ assertEquals("A", row0.get(1));
+ assertEquals("", row0.get(2));
+ final List<String> row1 = rows.get(1).getValues();
+ assertEquals(3, row1.size());
+ assertEquals("b", row1.get(0));
+ assertEquals("B", row1.get(1));
+ assertEquals("E", row1.get(2));
+ final List<String> row2 = rows.get(2).getValues();
+ assertEquals(3, row2.size());
+ assertEquals("c", row2.get(0));
+ assertEquals("C", row2.get(1));
+ assertEquals("", row2.get(2));
+ final List<String> row3 = rows.get(3).getValues();
+ assertEquals(3, row3.size());
+ assertEquals("d", row3.get(0));
+ assertEquals("", row3.get(1));
+ assertEquals("D", row3.get(2));
+ final List<String> row4 = rows.get(4).getValues();
+ assertEquals(3, row4.size());
+ assertEquals("f", row4.get(0));
+ assertEquals("", row4.get(1));
+ assertEquals("F", row4.get(2));
+ }
+
+ @Test
+ public void testFileTwice()
+ {
+ final IterativeTableModelBuilder builder = new IterativeTableModelBuilder("id");
+ final DatasetDescription description =
+ new DatasetDescription("code", "location", "sampleCode", "groupCode");
+ final DatasetFileLines lines =
+ new DatasetFileLines(new File("doesn't matter"), description, Arrays.asList(
+ "id\tval", "a\tA", "b\tB", "c\tC"));
+ builder.addFile(lines);
+ builder.addFile(lines);
+ final TableModel model = builder.getTableModel();
+ final List<TableModelColumnHeader> headers = model.getHeader();
+ assertEquals(3, headers.size());
+ assertEquals("id", headers.get(0).getTitle());
+ assertEquals(0, headers.get(0).getIndex());
+ assertEquals("val", headers.get(1).getTitle());
+ assertEquals(1, headers.get(1).getIndex());
+ assertEquals("valX", headers.get(2).getTitle());
+ assertEquals(2, headers.get(2).getIndex());
+ final List<TableModelRow> rows = model.getRows();
+ assertEquals(3, rows.size());
+ final List<String> row0 = rows.get(0).getValues();
+ assertEquals(3, row0.size());
+ assertEquals("a", row0.get(0));
+ assertEquals("A", row0.get(1));
+ assertEquals("A", row0.get(2));
+ final List<String> row1 = rows.get(1).getValues();
+ assertEquals(3, row1.size());
+ assertEquals("b", row1.get(0));
+ assertEquals("B", row1.get(1));
+ assertEquals("B", row1.get(2));
+ final List<String> row2 = rows.get(2).getValues();
+ assertEquals(3, row2.size());
+ assertEquals("c", row2.get(0));
+ assertEquals("C", row2.get(1));
+ assertEquals("C", row2.get(2));
+ }
+
+ @Test
+ public void testNoIdColumn()
+ {
+ final IterativeTableModelBuilder builder = new IterativeTableModelBuilder("id");
+ final DatasetDescription description =
+ new DatasetDescription("code", "location", "sampleCode", "groupCode");
+ final DatasetFileLines lines =
+ new DatasetFileLines(new File("bad file - no id"), description, Arrays.asList(
+ "ID\tval", "a\tA", "b\tB", "c\tC"));
+ builder.addFile(lines);
+ final TableModel model = builder.getTableModel();
+ assertEquals(0, model.getHeader().size());
+ assertEquals(0, model.getRows().size());
+ }
+
+ @Test
+ public void testTwoFilesNoIdColumnInOneFile()
+ {
+ final IterativeTableModelBuilder builder = new IterativeTableModelBuilder("id");
+ final DatasetDescription description =
+ new DatasetDescription("code", "location", "sampleCode", "groupCode");
+ final DatasetFileLines lines =
+ new DatasetFileLines(new File("bad file - no id (2)"), description, Arrays.asList(
+ "ID\tval", "a\tA", "b\tB", "c\tC"));
+ builder.addFile(lines);
+ final DatasetFileLines lines2 =
+ new DatasetFileLines(new File("doesn't matter"), description, Arrays.asList(
+ "id\tval", "a\tA", "b\tB", "c\tC"));
+ builder.addFile(lines2);
+ final TableModel model = builder.getTableModel();
+ final List<TableModelColumnHeader> headers = model.getHeader();
+ assertEquals(2, headers.size());
+ assertEquals("id", headers.get(0).getTitle());
+ assertEquals(0, headers.get(0).getIndex());
+ assertEquals("val", headers.get(1).getTitle());
+ assertEquals(1, headers.get(1).getIndex());
+ final List<TableModelRow> rows = model.getRows();
+ assertEquals(3, rows.size());
+ final List<String> row0 = rows.get(0).getValues();
+ assertEquals(2, row0.size());
+ assertEquals("a", row0.get(0));
+ assertEquals("A", row0.get(1));
+ final List<String> row1 = rows.get(1).getValues();
+ assertEquals(2, row1.size());
+ assertEquals("b", row1.get(0));
+ assertEquals("B", row1.get(1));
+ final List<String> row2 = rows.get(2).getValues();
+ assertEquals(2, row2.size());
+ assertEquals("c", row2.get(0));
+ assertEquals("C", row2.get(1));
+ }
+}
--
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