From fe8270010350f9d1c215d78b5e2db0702273c1dc Mon Sep 17 00:00:00 2001
From: gpawel <gpawel>
Date: Tue, 30 Aug 2011 12:45:31 +0000
Subject: [PATCH] LMS-2462 import from Excel files
SVN: 22710
---
.../cisd/common/filesystem/FileUtilities.java | 3 +-
.../common/parser/DefaultLineTokenizer.java | 6 +-
.../cisd/common/parser/DefaultParser.java | 28 +-
.../cisd/common/parser/ExcelFileLoader.java | 366 ++++++++++++++++++
.../systemsx/cisd/common/parser/ExcelRow.java | 69 ++++
.../cisd/common/parser/ExcelRowTokenizer.java | 87 +++++
.../cisd/common/parser/HeaderLineFilter.java | 6 +-
.../ch/systemsx/cisd/common/parser/ILine.java | 31 ++
.../cisd/common/parser/ILineTokenizer.java | 8 +-
.../systemsx/cisd/common/parser/IParser.java | 6 +-
.../ch/systemsx/cisd/common/parser/Line.java | 9 +-
.../cisd/common/parser/ParserUtilities.java | 16 +-
.../cisd/common/parser/TabFileLoader.java | 84 ++--
.../parser/filter/AlwaysAcceptLineFilter.java | 4 +-
.../ExcludeEmptyAndCommentLineFilter.java | 6 +-
.../common/parser/filter/ILineFilter.java | 4 +-
.../parser/filter/NonEmptyLineFilter.java | 6 +-
.../cisd/common/parser/DefaultParserTest.java | 78 ++--
.../common/parser/HeaderLineFilterTest.java | 22 +-
.../common/parser/ParserUtilitiesTest.java | 14 +-
.../java/MigrationStepExecutor.java | 10 +-
.../shared/parser/BisExcelFileLoader.java | 109 ++++++
.../shared/parser/ExcelFileSection.java | 167 ++++++++
.../parser/SampleUploadSectionsParser.java | 146 +++++--
.../parser/MaterialUploadSectionsParser.java | 147 +++++--
25 files changed, 1211 insertions(+), 221 deletions(-)
create mode 100644 common/source/java/ch/systemsx/cisd/common/parser/ExcelFileLoader.java
create mode 100644 common/source/java/ch/systemsx/cisd/common/parser/ExcelRow.java
create mode 100644 common/source/java/ch/systemsx/cisd/common/parser/ExcelRowTokenizer.java
create mode 100644 common/source/java/ch/systemsx/cisd/common/parser/ILine.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisExcelFileLoader.java
create mode 100644 openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/ExcelFileSection.java
diff --git a/common/source/java/ch/systemsx/cisd/common/filesystem/FileUtilities.java b/common/source/java/ch/systemsx/cisd/common/filesystem/FileUtilities.java
index dbe472c8751..2aed775d097 100644
--- a/common/source/java/ch/systemsx/cisd/common/filesystem/FileUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/filesystem/FileUtilities.java
@@ -59,6 +59,7 @@ import ch.systemsx.cisd.common.exceptions.FileExistsException;
import ch.systemsx.cisd.common.exceptions.UnknownLastChangedException;
import ch.systemsx.cisd.common.logging.ISimpleLogger;
import ch.systemsx.cisd.common.logging.LogLevel;
+import ch.systemsx.cisd.common.parser.Line;
import ch.systemsx.cisd.common.parser.filter.AlwaysAcceptLineFilter;
import ch.systemsx.cisd.common.parser.filter.ILineFilter;
import ch.systemsx.cisd.common.utilities.StringUtilities;
@@ -410,7 +411,7 @@ public final class FileUtilities
String line = reader.readLine();
for (int lineNumber = 0; line != null; ++lineNumber, line = reader.readLine())
{
- if (lineFilter.acceptLine(line, lineNumber))
+ if (lineFilter.acceptLine(new Line(lineNumber, line)))
{
list.add(line);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
index db16bc4b767..394bb680603 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultLineTokenizer.java
@@ -32,7 +32,7 @@ import org.apache.commons.lang.text.StrTokenizer;
*
* @author Christian Ribeaud
*/
-public class DefaultLineTokenizer implements ILineTokenizer
+public class DefaultLineTokenizer implements ILineTokenizer<String>
{
/** Allowed <code>Properties</code> keys. */
@@ -82,8 +82,8 @@ public class DefaultLineTokenizer implements ILineTokenizer
/**
* Sets a property for this <code>TabReaderParser</code>.
* <p>
- * Does nothing if given <code>key</code> is <code>null</code> and resets <code>key</code>
- * to default value if given <code>value</code> is <code>null</code>.
+ * Does nothing if given <code>key</code> is <code>null</code> and resets <code>key</code> to
+ * default value if given <code>value</code> is <code>null</code>.
* </p>
*/
public final void setProperty(PropertyKey key, String value)
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
index e715fc77493..014209e81f0 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/DefaultParser.java
@@ -32,24 +32,24 @@ import ch.systemsx.cisd.common.parser.filter.ILineFilter;
*
* @author Christian Ribeaud
*/
-public class DefaultParser<E> implements IParser<E>
+public class DefaultParser<E, T> implements IParser<E, T>
{
- private final ILineTokenizer lineTokenizer;
+ private final ILineTokenizer<T> lineTokenizer;
private IParserObjectFactory<E> factory;
/**
* Creates an instance based on the {@link DefaultLineTokenizer}.
*/
- public DefaultParser()
+ public static <E> DefaultParser<E, String> createDefaultParser()
{
- this(new DefaultLineTokenizer());
+ return new DefaultParser<E, String>(new DefaultLineTokenizer());
}
/**
* Creates an instance for the specified line tokenizer.
*/
- public DefaultParser(final ILineTokenizer lineTokenizer)
+ public DefaultParser(final ILineTokenizer<T> lineTokenizer)
{
this.lineTokenizer = lineTokenizer;
}
@@ -59,17 +59,17 @@ public class DefaultParser<E> implements IParser<E>
return factory.createObject(tokens);
}
- public final List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter,
+ public final List<E> parse(final Iterator<ILine<T>> lineIterator, final ILineFilter lineFilter,
final int headerLength) throws ParsingException
{
final List<E> elements = new ArrayList<E>();
lineTokenizer.init();
while (lineIterator.hasNext())
{
- final Line line = lineIterator.next();
- final String nextLine = line.getText();
+ final ILine<T> line = lineIterator.next();
+ final T nextLine = line.getObject();
final int number = line.getNumber();
- if (lineFilter.acceptLine(nextLine, number))
+ if (lineFilter.acceptLine(line))
{
E object = null;
String[] tokens = parseLine(number, nextLine, headerLength);
@@ -91,13 +91,13 @@ public class DefaultParser<E> implements IParser<E>
return elements;
}
- public final Iterator<E> parseIteratively(final Iterator<Line> lineIterator,
+ public final Iterator<E> parseIteratively(final Iterator<ILine<T>> lineIterator,
final ILineFilter lineFilter, final int headerLength) throws ParsingException
{
lineTokenizer.init();
return new Iterator<E>()
{
- Line currentLine = null;
+ ILine<T> currentLine = null;
public boolean hasNext()
{
@@ -105,7 +105,7 @@ public class DefaultParser<E> implements IParser<E>
while (hasNext)
{
currentLine = lineIterator.next();
- if (lineFilter.acceptLine(currentLine.getText(), currentLine.getNumber()))
+ if (lineFilter.acceptLine(currentLine))
{
break;
}
@@ -125,7 +125,7 @@ public class DefaultParser<E> implements IParser<E>
{
throw new NoSuchElementException();
}
- final String nextLine = currentLine.getText();
+ final T nextLine = currentLine.getObject();
final int number = currentLine.getNumber();
currentLine = null;
String[] tokens = parseLine(number, nextLine, headerLength);
@@ -151,7 +151,7 @@ public class DefaultParser<E> implements IParser<E>
this.factory = factory;
}
- private String[] parseLine(final int lineNumber, final String nextLine, final int headerLength)
+ private String[] parseLine(final int lineNumber, final T nextLine, final int headerLength)
{
String[] tokens = lineTokenizer.tokenize(nextLine);
if (tokens.length > headerLength)
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ExcelFileLoader.java b/common/source/java/ch/systemsx/cisd/common/parser/ExcelFileLoader.java
new file mode 100644
index 00000000000..c63545e93e2
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ExcelFileLoader.java
@@ -0,0 +1,366 @@
+/*
+ * Copyright 2007 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.common.parser;
+
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.HashSet;
+import java.util.Iterator;
+import java.util.List;
+import java.util.Map;
+import java.util.Set;
+import java.util.regex.Pattern;
+
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+
+import ch.systemsx.cisd.common.exceptions.NotImplementedException;
+import ch.systemsx.cisd.common.parser.filter.AlwaysAcceptLineFilter;
+import ch.systemsx.cisd.common.parser.filter.ILineFilter;
+
+/**
+ * Convenient class to load (or iterate over) a tab file, a reader or a stream. The loader delivers
+ * either a list or an iterator of beans of type <code>T</code>. The following formats for the
+ * column headers are recognized.
+ * <ol>
+ * <li>Column headers in first line:
+ *
+ * <pre>
+ * column1 column2 column2
+ * </pre>
+ * <li>Comment section:
+ *
+ * <pre>
+ * # 1. line of comment
+ * # 2. line of comment
+ * # ...
+ * column1 column2 column2
+ * </pre>
+ * <li>Column headers at the end of the comment section:
+ *
+ * <pre>
+ * # 1. line of comment
+ * # 2. line of comment
+ * # ...
+ * #
+ * #column1 column2 column2
+ * </pre>
+ *
+ * </ol>
+ *
+ * @author Franz-Josef Elmer
+ */
+public class ExcelFileLoader<T>
+{
+ public static final String COMMENT_PREFIX = "#";
+
+ // Excel can put comments in double quotes (") if they contain quote character. Multiple saving
+ // of the can cause multiple '"' to occure before the '#' character.
+ public static final Pattern COMMENT_REGEXP_PATTERN = Pattern.compile("\"*#.*");
+
+ public static final String DEFAULT_SECTION = "[DEFAULT]";
+
+ private final IParserObjectFactoryFactory<T> factory;
+
+ /**
+ * Creates a new instance based on the factory which uses only bean annotations.
+ */
+ public ExcelFileLoader(final Class<T> beanClass)
+ {
+ this.factory = new IParserObjectFactoryFactory<T>()
+ {
+ public IParserObjectFactory<T> createFactory(IPropertyMapper propertyMapper)
+ throws ParserException
+ {
+ return new AbstractParserObjectFactory<T>(beanClass, propertyMapper)
+ {
+ };
+ }
+ };
+ }
+
+ /**
+ * Creates a new instance based on the specified factory.
+ */
+ public ExcelFileLoader(final IParserObjectFactoryFactory<T> factory)
+ {
+ assert factory != null : "Undefined factory";
+ this.factory = factory;
+ }
+
+ /**
+ * Loads data from the specified reader.
+ * <p>
+ * The header can contain comments which are ignored. The column names can be the first
+ * uncommented line or the last commented line. The latter case is determined by the fact, that
+ * the one before the last line is a single hash.
+ * </p>
+ */
+ public List<T> load(final Sheet sheet, int begin, int end, Map<String, String> defaults)
+ throws ParserException, ParsingException, IllegalArgumentException
+ {
+ assert sheet != null : "Unspecified reader";
+
+ final Iterator<ILine<Row>> rowIterator = createRowIterator(sheet, begin, end);
+ return load(rowIterator, defaults);
+ }
+
+ public static final Map<String, String> parseDefaults(Sheet sheet, int begin, int end)
+ {
+ final Iterator<ILine<Row>> lineIterator = createRowIterator(sheet, begin, end);
+ final Map<String, String> defaults = new HashMap<String, String>();
+ return parseDefaults(lineIterator, defaults);
+ }
+
+ private static final Map<String, String> parseDefaults(final Iterator<ILine<Row>> rowIterator,
+ final Map<String, String> defaults)
+ {
+ while (rowIterator.hasNext())
+ {
+ ILine<Row> row = rowIterator.next();
+ if (startsDefaultSection(row))
+ {
+ break;
+ }
+
+ String[] tokens = ExcelRowTokenizer.tokenizeRow(row.getObject());
+ if (tokens.length >= 2)
+ {
+ String name = tokens[0];
+ String value = tokens[1];
+ defaults.put(name.toLowerCase(), value);
+ }
+ }
+
+ return defaults;
+ }
+
+ private List<T> load(final Iterator<ILine<Row>> lineIterator, Map<String, String> fileDefaults)
+ {
+ ILine<Row> previousLine = null;
+ ILine<Row> line = null;
+ boolean previousLineHasColumnHeaders = false;
+
+ Map<String, String> defaults = new HashMap<String, String>(fileDefaults);
+ while (lineIterator.hasNext())
+ {
+ previousLineHasColumnHeaders = (previousLine != null) && isComment(previousLine);
+ previousLine = line;
+ line = lineIterator.next();
+ if (isComment(line))
+ {
+ continue;
+ } else if (startsDefaultSection(line))
+ {
+ parseDefaults(lineIterator, defaults);
+ line = previousLine = null;
+ previousLineHasColumnHeaders = false;
+ } else if (isComment(line) == false)
+ {
+ break;
+ }
+ }
+
+ if (line == null) // no lines present
+ {
+ return new ArrayList<T>();
+ }
+
+ Row headerRow = null;
+ if (previousLineHasColumnHeaders && (previousLine != null /* just for eclipse */))
+ {
+ headerRow = trimComment(previousLine);
+ } else
+ {
+ headerRow = line.getObject();
+ }
+
+ final IParser<T, Row> parser = createParser();
+ final String[] tokens = ExcelRowTokenizer.tokenizeRow(headerRow);
+ final int headerLength = tokens.length;
+ notUnique(tokens);
+
+ final IPropertyMapper propertyMapper = new DefaultPropertyMapper(tokens, defaults);
+ parser.setObjectFactory(factory.createFactory(propertyMapper));
+
+ ILine<Row> firstContentLine = previousLineHasColumnHeaders ? line : null;
+ Iterator<ILine<Row>> contentLineIterator =
+ createContentIterator(firstContentLine, lineIterator);
+ final ILineFilter filter = AlwaysAcceptLineFilter.INSTANCE;
+ return parser.parse(contentLineIterator, filter, headerLength);
+ }
+
+ private static boolean startsDefaultSection(Row row)
+ {
+ Cell cell = row.getCell(0);
+ if (cell == null || cell.getCellType() != Cell.CELL_TYPE_STRING)
+ {
+ return false;
+ } else
+ {
+ return DEFAULT_SECTION.equals(cell.getStringCellValue());
+ }
+ }
+
+ private static boolean startsDefaultSection(ILine<Row> row)
+ {
+ return startsDefaultSection(row.getObject());
+ }
+
+ private static Row trimComment(ILine<Row> previousLine)
+ {
+ if (isComment(previousLine))
+ {
+ Cell firstCell = previousLine.getObject().getCell(0);
+ firstCell.setCellValue(firstCell.getStringCellValue()
+ .substring(COMMENT_PREFIX.length()));
+ }
+ return previousLine.getObject();
+ }
+
+ private static boolean isComment(ILine<Row> line)
+ {
+ Row row = line.getObject();
+ return row.getCell(0) != null && row.getCell(0).toString().startsWith(COMMENT_PREFIX);
+ }
+
+ /**
+ * @param firstContentLineOrNull if not null, it will be returned as the first iterator element,
+ * followed by all iterator elements from the second parameter
+ */
+ private static Iterator<ILine<Row>> createContentIterator(
+ final ILine<Row> firstContentLineOrNull, final Iterator<ILine<Row>> lineIterator)
+ {
+ return new Iterator<ILine<Row>>()
+ {
+ private ILine<Row> firstLineOrNull = firstContentLineOrNull;
+
+ public boolean hasNext()
+ {
+ return firstLineOrNull != null || lineIterator.hasNext();
+ }
+
+ public ILine<Row> next()
+ {
+ return nextLine();
+ }
+
+ private ILine<Row> nextLine()
+ {
+ if (firstLineOrNull != null)
+ {
+ ILine<Row> line = firstLineOrNull;
+ firstLineOrNull = null;
+ return line;
+ } else
+ {
+ return lineIterator.next();
+ }
+ }
+
+ public void remove()
+ {
+ throw new NotImplementedException();
+ }
+ };
+ }
+
+ private static Iterator<ILine<Row>> createRowIterator(Sheet sheet, int begin, int end)
+ {
+ return new ExcelFileRowIterator(sheet, begin, end);
+ }
+
+ /**
+ * Checks given <var>tokens</var> whether there is no duplicate.
+ * <p>
+ * Note that the search is case-insensitive.
+ * </p>
+ *
+ * @throws IllegalArgumentException if there is at least one duplicate in the given
+ * <var>tokens</var>.
+ */
+ private final static void notUnique(final String[] tokens)
+ {
+ assert tokens != null : "Given tokens can not be null.";
+ final Set<String> unique = new HashSet<String>();
+ for (final String token : tokens)
+ {
+ if (unique.add(token.toLowerCase()) == false)
+ {
+ throw new IllegalArgumentException(String.format("Duplicated column name '%s'.",
+ token));
+ }
+ }
+ }
+
+ private final <E> IParser<E, Row> createParser()
+ {
+ ExcelRowTokenizer tokenizer = new ExcelRowTokenizer();
+ return new DefaultParser<E, Row>(tokenizer);
+ }
+
+ //
+ // Helper classes
+ //
+ private final static class ExcelFileRowIterator implements Iterator<ILine<Row>>
+ {
+ private final Sheet sheet;
+
+ private int current;
+
+ private final int end;
+
+ private ExcelFileRowIterator(Sheet sheet, int begin, int end)
+ {
+ this.sheet = sheet;
+ this.current = begin;
+ this.end = end;
+ getFirstNonEmptyCurrent();
+ }
+
+ private void getFirstNonEmptyCurrent()
+ {
+ while (sheet.getRow(current) == null && current <= end)
+ {
+ current++;
+ }
+ }
+
+ public final void remove()
+ {
+ throw new UnsupportedOperationException();
+ }
+
+ public final ILine<Row> next()
+ {
+ try
+ {
+ return new ExcelRow(sheet.getRow(current));
+ } finally
+ {
+ current++;
+ getFirstNonEmptyCurrent();
+ }
+ }
+
+ public final boolean hasNext()
+ {
+ return current <= end;
+ }
+ }
+}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ExcelRow.java b/common/source/java/ch/systemsx/cisd/common/parser/ExcelRow.java
new file mode 100644
index 00000000000..545a43d51e7
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ExcelRow.java
@@ -0,0 +1,69 @@
+/*
+ * Copyright 2011 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.common.parser;
+
+import org.apache.poi.ss.usermodel.Row;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ExcelRow implements ILine<Row>
+{
+ private Row row;
+
+ private String text;
+
+ public ExcelRow(Row row)
+ {
+ this.row = row;
+ }
+
+ public String getText()
+ {
+ if (text == null)
+ {
+ text = toString(row);
+ }
+ return text;
+ }
+
+ public int getNumber()
+ {
+ return row.getRowNum();
+ }
+
+ public Row getObject()
+ {
+ return row;
+ }
+
+ private static String toString(Row row)
+ {
+ StringBuilder sb = new StringBuilder();
+
+ for (String s : new ExcelRowTokenizer().tokenize(row))
+ {
+ if (s.length() > 0)
+ {
+ sb.append("\t");
+ }
+ sb.append(s);
+ }
+
+ return sb.toString();
+ }
+}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ExcelRowTokenizer.java b/common/source/java/ch/systemsx/cisd/common/parser/ExcelRowTokenizer.java
new file mode 100644
index 00000000000..5be83b61689
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ExcelRowTokenizer.java
@@ -0,0 +1,87 @@
+/*
+ * Copyright 2011 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.common.parser;
+
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.util.CellReference;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ExcelRowTokenizer implements ILineTokenizer<Row>
+{
+ public void init()
+ {
+ }
+
+ public String[] tokenize(Row row)
+ {
+ return tokenizeRow(row);
+ }
+
+ public static String[] tokenizeRow(Row row)
+ {
+ String[] line = new String[row.getLastCellNum()];
+ for (Cell cell : row)
+ {
+ String value = extractCellValue(cell);
+ line[cell.getColumnIndex()] = value;
+ }
+
+ return line;
+ }
+
+ private static String extractCellValue(Cell cell)
+ {
+ switch (cell.getCellType())
+ {
+ case Cell.CELL_TYPE_BLANK:
+ return "BLANK";
+ case Cell.CELL_TYPE_BOOLEAN:
+ return Boolean.toString(cell.getBooleanCellValue());
+ case Cell.CELL_TYPE_NUMERIC:
+ return Double.toString(cell.getNumericCellValue());
+ case Cell.CELL_TYPE_STRING:
+ return cell.getStringCellValue();
+ case Cell.CELL_TYPE_FORMULA:
+ throw new UserFailureException(
+ "Excel formulas are not supported but one was found in cell "
+ + extractCellPosition(cell));
+ case Cell.CELL_TYPE_ERROR:
+ throw new UserFailureException("There is an error in cell "
+ + extractCellPosition(cell));
+ default:
+ throw new UserFailureException("Unknown data type of cell "
+ + extractCellPosition(cell));
+ }
+ }
+
+ /** @return cell coordinates in Excel style (e.g. D5) */
+ private static String extractCellPosition(Cell cell)
+ {
+ String col = CellReference.convertNumToColString(cell.getColumnIndex());
+ String row = "" + (cell.getRowIndex() + 1);
+ return col + row;
+ }
+
+ public void destroy()
+ {
+ }
+}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
index 5701c069f1b..08837e5ebc1 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/HeaderLineFilter.java
@@ -54,10 +54,10 @@ public final class HeaderLineFilter implements ILineFilter
// LineFilter
//
- public final boolean acceptLine(String line, int lineNumber)
+ public final <T> boolean acceptLine(ILine<T> line)
{
- if (ExcludeEmptyAndCommentLineFilter.INSTANCE.acceptLine(line, lineNumber) == false
- || lineNumber == headerLineNumber)
+ if (ExcludeEmptyAndCommentLineFilter.INSTANCE.acceptLine(line) == false
+ || line.getNumber() == headerLineNumber)
{
return false;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ILine.java b/common/source/java/ch/systemsx/cisd/common/parser/ILine.java
new file mode 100644
index 00000000000..db46e9cd992
--- /dev/null
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ILine.java
@@ -0,0 +1,31 @@
+/*
+ * Copyright 2008 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.common.parser;
+
+/**
+ * A small object that represents a line in a <code>File</code> context.
+ *
+ * @author Pawel Glyzewski
+ */
+public interface ILine<T>
+{
+ public String getText();
+
+ public int getNumber();
+
+ public T getObject();
+}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java b/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
index de749399a5d..91b7f82d504 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ILineTokenizer.java
@@ -17,12 +17,12 @@
package ch.systemsx.cisd.common.parser;
/**
- * A <code>ILineTokenizer</code> implementation is able to split a given <code>String</code>
- * line in an array of tokens.
+ * A <code>ILineTokenizer</code> implementation is able to split a given <code>T</code> line in an
+ * array of tokens.
*
* @author Christian Ribeaud
*/
-public interface ILineTokenizer
+public interface ILineTokenizer<T>
{
/**
@@ -34,7 +34,7 @@ public interface ILineTokenizer
public void init();
/** Splits given <code>line</code> into an array of tokens. */
- public String[] tokenize(String line);
+ public String[] tokenize(T line);
/**
* Cleans up resources used by this <code>ILineTokenizer</code>.
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
index 62de1595e0e..8912dff0c8c 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/IParser.java
@@ -27,7 +27,7 @@ import ch.systemsx.cisd.common.parser.filter.ILineFilter;
*
* @author Christian Ribeaud
*/
-public interface IParser<E>
+public interface IParser<E, T>
{
/**
@@ -38,7 +38,7 @@ public interface IParser<E>
* @param headerLength number of columns in the header
* @return a <code>List</code> of elements.
*/
- public List<E> parse(final Iterator<Line> lineIterator, final ILineFilter lineFilter,
+ public List<E> parse(final Iterator<ILine<T>> lineIterator, final ILineFilter lineFilter,
final int headerLength) throws ParsingException;
/**
@@ -51,7 +51,7 @@ public interface IParser<E>
* @param headerLength number of columns in the header
* @return an <code>List</code> of elements.
*/
- public Iterator<E> parseIteratively(final Iterator<Line> lineIterator,
+ public Iterator<E> parseIteratively(final Iterator<ILine<T>> lineIterator,
final ILineFilter lineFilter, final int headerLength) throws ParsingException;
/**
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/Line.java b/common/source/java/ch/systemsx/cisd/common/parser/Line.java
index dfcd0d41157..2e8745e063e 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/Line.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/Line.java
@@ -21,13 +21,13 @@ package ch.systemsx.cisd.common.parser;
*
* @author Christian Ribeaud
*/
-public final class Line
+public final class Line implements ILine<String>
{
private final String text;
private final int number;
- Line(final int number, final String text)
+ public Line(final int number, final String text)
{
assert text != null : "Unspecified text.";
this.number = number;
@@ -44,4 +44,9 @@ public final class Line
return number;
}
+ public String getObject()
+ {
+ return text;
+ }
+
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java b/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
index 6721c422f3f..0778dd90ee4 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/ParserUtilities.java
@@ -59,6 +59,7 @@ public final class ParserUtilities
{
this(content, null);
}
+
public LineSplitter(final String content, final ILineFilter lineFilterOrNull)
{
assert content != null : "Unspecified context.";
@@ -72,7 +73,7 @@ public final class ParserUtilities
{
this(file, null);
}
-
+
public LineSplitter(final File file, final ILineFilter lineFilterOrNull)
throws IOExceptionUnchecked
{
@@ -93,7 +94,7 @@ public final class ParserUtilities
return (lineFilterOrNull == null) ? AlwaysAcceptLineFilter.INSTANCE : lineFilterOrNull;
}
- public void close()
+ public void close()
{
lineIterator.close();
}
@@ -101,15 +102,16 @@ public final class ParserUtilities
/**
* Returns the next line that is accepted by the <var>lineFilter</var>.
*/
- public Line tryNextLine()
+ public ILine<String> tryNextLine()
{
for (int line = lineNumber; lineIterator.hasNext(); line++)
{
final String nextLine = lineIterator.nextLine();
- if (lineFilter.acceptLine(nextLine, line))
+ final Line ret = new Line(line, nextLine);
+ if (lineFilter.acceptLine(ret))
{
lineNumber = line + 1;
- return new Line(line, nextLine);
+ return ret;
}
}
return null;
@@ -128,7 +130,7 @@ public final class ParserUtilities
* @param content the content that is going to be analyzed. Can not be <code>null</code>.
* @return <code>null</code> if all lines have been filtered out.
*/
- public final static Line tryGetFirstAcceptedLine(final String content,
+ public final static ILine<String> tryGetFirstAcceptedLine(final String content,
final ILineFilter lineFilterOrNull)
{
final LineSplitter splitter = new LineSplitter(content, lineFilterOrNull);
@@ -154,7 +156,7 @@ public final class ParserUtilities
* exists.
* @return <code>null</code> if all lines have been filtered out.
*/
- public final static Line tryGetFirstAcceptedLine(final File file,
+ public final static ILine<String> tryGetFirstAcceptedLine(final File file,
final ILineFilter lineFilterOrNull)
{
final LineSplitter splitter = new LineSplitter(file, lineFilterOrNull);
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
index c47a095b455..4dea725e2cd 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/TabFileLoader.java
@@ -184,7 +184,7 @@ public class TabFileLoader<T>
{
assert reader != null : "Unspecified reader";
- final Iterator<Line> lineIterator = createLineIterator(reader);
+ final Iterator<ILine<String>> lineIterator = createLineIterator(reader);
return iterate(lineIterator, defaults);
}
@@ -201,7 +201,7 @@ public class TabFileLoader<T>
{
assert reader != null : "Unspecified reader";
- final Iterator<Line> lineIterator = createLineIterator(reader);
+ final Iterator<ILine<String>> lineIterator = createLineIterator(reader);
return load(lineIterator, defaults);
}
@@ -220,7 +220,7 @@ public class TabFileLoader<T>
try
{
- final Iterator<Line> lineIterator = createLineIterator(stream);
+ final Iterator<ILine<String>> lineIterator = createLineIterator(stream);
return iterate(lineIterator, defaults);
} catch (IOException ex)
{
@@ -243,7 +243,7 @@ public class TabFileLoader<T>
try
{
- final Iterator<Line> lineIterator = createLineIterator(stream);
+ final Iterator<ILine<String>> lineIterator = createLineIterator(stream);
return load(lineIterator, defaults);
} catch (IOException ex)
{
@@ -253,17 +253,17 @@ public class TabFileLoader<T>
public static final Map<String, String> parseDefaults(Reader reader)
{
- final Iterator<Line> lineIterator = createLineIterator(reader);
+ final Iterator<ILine<String>> lineIterator = createLineIterator(reader);
final Map<String, String> defaults = new HashMap<String, String>();
return parseDefaults(lineIterator, defaults);
}
- private static final Map<String, String> parseDefaults(final Iterator<Line> lineIterator,
- final Map<String, String> defaults)
+ private static final Map<String, String> parseDefaults(
+ final Iterator<ILine<String>> lineIterator, final Map<String, String> defaults)
{
while (lineIterator.hasNext())
{
- Line line = lineIterator.next();
+ ILine<String> line = lineIterator.next();
String text = line.getText();
if (DEFAULT_SECTION.equals(text))
{
@@ -281,10 +281,11 @@ public class TabFileLoader<T>
return defaults;
}
- private List<T> load(final Iterator<Line> lineIterator, Map<String, String> fileDefaults)
+ private List<T> load(final Iterator<ILine<String>> lineIterator,
+ Map<String, String> fileDefaults)
{
- Line previousLine = null;
- Line line = null;
+ ILine<String> previousLine = null;
+ ILine<String> line = null;
boolean previousLineHasColumnHeaders = false;
Map<String, String> defaults = new HashMap<String, String>(fileDefaults);
@@ -321,7 +322,7 @@ public class TabFileLoader<T>
headerLine = line.getText();
}
- final IParser<T> parser = createParser();
+ final IParser<T, String> parser = createParser();
final String[] tokens = StringUtils.split(headerLine, TOKENS_SEPARATOR);
int lastEmptyHeadersToSkip = countLastEmptyTokens(headerLine);
final int headerLength = tokens.length;
@@ -330,17 +331,18 @@ public class TabFileLoader<T>
final IPropertyMapper propertyMapper = new DefaultPropertyMapper(tokens, defaults);
parser.setObjectFactory(factory.createFactory(propertyMapper));
- Line firstContentLine = previousLineHasColumnHeaders ? line : null;
- Iterator<Line> contentLineIterator =
+ ILine<String> firstContentLine = previousLineHasColumnHeaders ? line : null;
+ Iterator<ILine<String>> contentLineIterator =
createContentIterator(firstContentLine, lineIterator, lastEmptyHeadersToSkip);
final ILineFilter filter = AlwaysAcceptLineFilter.INSTANCE;
return parser.parse(contentLineIterator, filter, headerLength);
}
- private Iterator<T> iterate(final Iterator<Line> lineIterator, Map<String, String> fileDefaults)
+ private Iterator<T> iterate(final Iterator<ILine<String>> lineIterator,
+ Map<String, String> fileDefaults)
{
- Line previousLine = null;
- Line line = null;
+ ILine<String> previousLine = null;
+ ILine<String> line = null;
boolean previousLineHasColumnHeaders = false;
Map<String, String> defaults = new HashMap<String, String>(fileDefaults);
@@ -393,7 +395,7 @@ public class TabFileLoader<T>
headerLine = line.getText();
}
- final IParser<T> parser = createParser();
+ final IParser<T, String> parser = createParser();
final String[] tokens = StringUtils.split(headerLine, TOKENS_SEPARATOR);
int lastEmptyHeadersToSkip = countLastEmptyTokens(headerLine);
final int headerLength = tokens.length;
@@ -402,26 +404,26 @@ public class TabFileLoader<T>
final IPropertyMapper propertyMapper = new DefaultPropertyMapper(tokens, defaults);
parser.setObjectFactory(factory.createFactory(propertyMapper));
- Line firstContentLine = previousLineHasColumnHeaders ? line : null;
- Iterator<Line> contentLineIterator =
+ ILine<String> firstContentLine = previousLineHasColumnHeaders ? line : null;
+ Iterator<ILine<String>> contentLineIterator =
createContentIterator(firstContentLine, lineIterator, lastEmptyHeadersToSkip);
final ILineFilter filter = AlwaysAcceptLineFilter.INSTANCE;
return parser.parseIteratively(contentLineIterator, filter, headerLength);
}
- private static boolean startsDefaultSection(Line line)
+ private static boolean startsDefaultSection(ILine<String> line)
{
String text = line.getText();
return DEFAULT_SECTION.equals(text);
}
- private static boolean startsWithComment(Line line)
+ private static boolean startsWithComment(ILine<String> line)
{
String text = line.getText();
return COMMENT_REGEXP_PATTERN.matcher(text).matches();
}
- private static String trimComment(Line previousLine)
+ private static String trimComment(ILine<String> previousLine)
{
String text = previousLine.getText().trim();
if (text.startsWith(COMMENT_PREFIX))
@@ -433,7 +435,7 @@ public class TabFileLoader<T>
}
}
- private static boolean isComment(Line line)
+ private static boolean isComment(ILine<String> line)
{
String text = line.getText();
return COMMENT_PREFIX.equals(text);
@@ -445,26 +447,27 @@ public class TabFileLoader<T>
* @param lastEmptyTokensToSkip the number of token separators which will be removed form the
* end of each iterated line
*/
- private static Iterator<Line> createContentIterator(final Line firstContentLineOrNull,
- final Iterator<Line> lineIterator, final int lastEmptyTokensToSkip)
+ private static Iterator<ILine<String>> createContentIterator(
+ final ILine<String> firstContentLineOrNull, final Iterator<ILine<String>> lineIterator,
+ final int lastEmptyTokensToSkip)
{
final String suffixToDelete = multiply(lastEmptyTokensToSkip, TOKENS_SEPARATOR);
- return new Iterator<Line>()
+ return new Iterator<ILine<String>>()
{
- private Line firstLineOrNull = firstContentLineOrNull;
+ private ILine<String> firstLineOrNull = firstContentLineOrNull;
public boolean hasNext()
{
return firstLineOrNull != null || lineIterator.hasNext();
}
- public Line next()
+ public ILine<String> next()
{
return trim(nextUntrimmed());
}
- private Line trim(Line line)
+ private ILine<String> trim(ILine<String> line)
{
if (lastEmptyTokensToSkip == 0)
{
@@ -496,11 +499,11 @@ public class TabFileLoader<T>
}
}
- private Line nextUntrimmed()
+ private ILine<String> nextUntrimmed()
{
if (firstLineOrNull != null)
{
- Line line = firstLineOrNull;
+ ILine<String> line = firstLineOrNull;
firstLineOrNull = null;
return line;
} else
@@ -539,18 +542,19 @@ public class TabFileLoader<T>
return counter;
}
- private static Iterator<Line> createLineIterator(final Reader reader)
+ private static Iterator<ILine<String>> createLineIterator(final Reader reader)
{
final LineIterator lineIterator = IOUtils.lineIterator(reader);
- final Iterator<Line> iterator = new TabFileLineIterator(lineIterator);
+ final Iterator<ILine<String>> iterator = new TabFileLineIterator(lineIterator);
return iterator;
}
- private static Iterator<Line> createLineIterator(final InputStream stream) throws IOException
+ private static Iterator<ILine<String>> createLineIterator(final InputStream stream)
+ throws IOException
{
final LineIterator lineIterator =
IOUtils.lineIterator(stream, UnicodeUtils.DEFAULT_UNICODE_CHARSET);
- final Iterator<Line> iterator = new TabFileLineIterator(lineIterator);
+ final Iterator<ILine<String>> iterator = new TabFileLineIterator(lineIterator);
return iterator;
}
@@ -577,19 +581,19 @@ public class TabFileLoader<T>
}
}
- private final <E> IParser<E> createParser()
+ private final <E> IParser<E, String> createParser()
{
DefaultLineTokenizer tokenizer = new DefaultLineTokenizer();
// recognize default Excel text qualifiers
tokenizer.setProperty(PropertyKey.QUOTE_CHARS, "'\"");
- return new DefaultParser<E>(tokenizer);
+ return new DefaultParser<E, String>(tokenizer);
}
//
// Helper classes
//
- private final static class TabFileLineIterator implements Iterator<Line>
+ private final static class TabFileLineIterator implements Iterator<ILine<String>>
{
private final LineIterator lineIterator;
@@ -610,7 +614,7 @@ public class TabFileLoader<T>
lineIterator.remove();
}
- public final Line next()
+ public final ILine<String> next()
{
return new Line(++lineNumber, lineIterator.nextLine());
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/filter/AlwaysAcceptLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/filter/AlwaysAcceptLineFilter.java
index 6b9a72647b1..309684912c6 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/filter/AlwaysAcceptLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/filter/AlwaysAcceptLineFilter.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.common.parser.filter;
+import ch.systemsx.cisd.common.parser.ILine;
+
/**
* A default line filter that accepts any line.
*
@@ -33,7 +35,7 @@ public final class AlwaysAcceptLineFilter implements ILineFilter
// ILineFilter
//
- public final boolean acceptLine(final String line, final int lineNumber)
+ public final <T> boolean acceptLine(ILine<T> line)
{
return true;
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/filter/ExcludeEmptyAndCommentLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/filter/ExcludeEmptyAndCommentLineFilter.java
index 91b12e2262f..3b029bbd75c 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/filter/ExcludeEmptyAndCommentLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/filter/ExcludeEmptyAndCommentLineFilter.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.common.parser.filter;
+import ch.systemsx.cisd.common.parser.ILine;
+
/**
* A default <code>LineFilter</code> implementation that excludes empty and comment lines.
* <p>
@@ -36,10 +38,10 @@ public final class ExcludeEmptyAndCommentLineFilter implements ILineFilter
// ILineFilter
//
- public final boolean acceptLine(final String line, final int lineNumber)
+ public final <T> boolean acceptLine(ILine<T> line)
{
assert line != null : "Unspecified line";
- final String trimmed = line.trim();
+ final String trimmed = line.getText().trim();
return trimmed.length() > 0 && trimmed.startsWith("#") == false;
}
}
\ No newline at end of file
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/filter/ILineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/filter/ILineFilter.java
index 5c2e5cad8ff..7f66d1afda0 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/filter/ILineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/filter/ILineFilter.java
@@ -16,6 +16,8 @@
package ch.systemsx.cisd.common.parser.filter;
+import ch.systemsx.cisd.common.parser.ILine;
+
/**
* A line filter for <code>ReaderParser</code>.
*
@@ -29,5 +31,5 @@ public interface ILineFilter
*
* @param line the line read from the <code>Reader</code>. Can not be <code>null</code>.
*/
- public boolean acceptLine(final String line, final int lineNumber);
+ public <T> boolean acceptLine(final ILine<T> line);
}
diff --git a/common/source/java/ch/systemsx/cisd/common/parser/filter/NonEmptyLineFilter.java b/common/source/java/ch/systemsx/cisd/common/parser/filter/NonEmptyLineFilter.java
index 431073d753c..969b005824b 100644
--- a/common/source/java/ch/systemsx/cisd/common/parser/filter/NonEmptyLineFilter.java
+++ b/common/source/java/ch/systemsx/cisd/common/parser/filter/NonEmptyLineFilter.java
@@ -17,6 +17,8 @@ package ch.systemsx.cisd.common.parser.filter;
import org.apache.commons.lang.StringUtils;
+import ch.systemsx.cisd.common.parser.ILine;
+
/**
* A default <code>LineFilter</code> implementation that excludes empty lines.
*
@@ -34,8 +36,8 @@ public final class NonEmptyLineFilter implements ILineFilter
// ILineFilter
//
- public final boolean acceptLine(final String line, final int lineNumber)
+ public final <T> boolean acceptLine(ILine<T> line)
{
- return StringUtils.isNotBlank(line);
+ return StringUtils.isNotBlank(line.getText());
}
}
\ No newline at end of file
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
index 8b083ef7993..4b0b19824a9 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/DefaultParserTest.java
@@ -16,7 +16,10 @@
package ch.systemsx.cisd.common.parser;
-import static org.testng.AssertJUnit.*;
+import static org.testng.AssertJUnit.assertEquals;
+import static org.testng.AssertJUnit.assertFalse;
+import static org.testng.AssertJUnit.assertTrue;
+import static org.testng.AssertJUnit.fail;
import java.util.Arrays;
import java.util.Iterator;
@@ -31,25 +34,24 @@ import org.testng.annotations.Test;
*/
public final class DefaultParserTest
{
- private final static List<String> text =
- Arrays.asList("", "# This is a comment", "firstName\tlastName\taddress\tcity",
- "Charles\tDarwin\tHumboldt Ave. 1865\t4242 Somewhere",
- "Albert\tEinstein\tNewton Road 1905\t4711 Princton");
+ private final static List<String> text = Arrays.asList("", "# This is a comment",
+ "firstName\tlastName\taddress\tcity",
+ "Charles\tDarwin\tHumboldt Ave. 1865\t4242 Somewhere",
+ "Albert\tEinstein\tNewton Road 1905\t4711 Princton");
- private final static List<String> textWithTab =
- Arrays.asList("", "# This is a comment", "firstName\tlastName\taddress\tcity",
- "Charles\tDarwin\tHumboldt Ave. 1865\t4242 Somewhere",
- "Albert\t\tNewton Road 1905\t");
+ private final static List<String> textWithTab = Arrays.asList("", "# This is a comment",
+ "firstName\tlastName\taddress\tcity",
+ "Charles\tDarwin\tHumboldt Ave. 1865\t4242 Somewhere", "Albert\t\tNewton Road 1905\t");
- private final static List<String> textWithMissingLastCells =
- Arrays.asList("", "# This is a comment", "firstName\tlastName\taddress\tcity",
- "\tDarwin\tHumboldt Ave. 1865", "Albert\tEinstein");
+ private final static List<String> textWithMissingLastCells = Arrays.asList("",
+ "# This is a comment", "firstName\tlastName\taddress\tcity",
+ "\tDarwin\tHumboldt Ave. 1865", "Albert\tEinstein");
private final static int HEADER_LENGTH = 4;
- private final static IParser<String[]> createParser()
+ private final static IParser<String[], String> createParser()
{
- final IParser<String[]> parser = new DefaultParser<String[]>();
+ final IParser<String[], String> parser = DefaultParser.createDefaultParser();
parser.setObjectFactory(IParserObjectFactory.STRING_ARRAY_OBJECT_FACTORY);
return parser;
}
@@ -57,7 +59,7 @@ public final class DefaultParserTest
@Test
public final void testParseWithoutFactoryAndHeader()
{
- final IParser<String[]> parser = createParser();
+ final IParser<String[], String> parser = createParser();
final List<String[]> result =
parser.parse(createLineIterator(text), new HeaderLineFilter(), HEADER_LENGTH);
assertEquals(3, result.size());
@@ -70,7 +72,7 @@ public final class DefaultParserTest
@Test
public final void testParseIterativelyWithoutFactoryAndHeader()
{
- final IParser<String[]> parser = createParser();
+ final IParser<String[], String> parser = createParser();
final Iterator<String[]> result =
parser.parseIteratively(createLineIterator(text), new HeaderLineFilter(),
HEADER_LENGTH);
@@ -89,7 +91,7 @@ public final class DefaultParserTest
@Test
public final void testParseWithoutFactoryWithLineFilter()
{
- final IParser<String[]> parser = createParser();
+ final IParser<String[], String> parser = createParser();
final List<String[]> result =
parser.parse(createLineIterator(text), new HeaderLineFilter(3), HEADER_LENGTH);
assertEquals(2, result.size());
@@ -100,11 +102,9 @@ public final class DefaultParserTest
@Test
public final void testParseFileWithTabs()
{
- final IParser<String[]> parser = createParser();
+ final IParser<String[], String> parser = createParser();
final List<String[]> result =
- parser
- .parse(createLineIterator(textWithTab), new HeaderLineFilter(),
- HEADER_LENGTH);
+ parser.parse(createLineIterator(textWithTab), new HeaderLineFilter(), HEADER_LENGTH);
assertEquals(3, result.size());
assertEquals("Albert", result.get(2)[0]);
assertEquals("", result.get(2)[1]);
@@ -115,7 +115,7 @@ public final class DefaultParserTest
@Test
public final void testParseFileWithMissingLastCells()
{
- final IParser<String[]> parser = createParser();
+ final IParser<String[], String> parser = createParser();
final List<String[]> result =
parser.parse(createLineIterator(textWithMissingLastCells), new HeaderLineFilter(),
HEADER_LENGTH);
@@ -133,7 +133,7 @@ public final class DefaultParserTest
@Test
public final void testParseWithColumnSizeMismatching()
{
- final IParser<String[]> parser = createParser();
+ final IParser<String[], String> parser = createParser();
try
{
parser.parse(createLineIterator(text), new HeaderLineFilter(3), HEADER_LENGTH + 1);
@@ -149,18 +149,20 @@ public final class DefaultParserTest
@Test
public final void testCreateObjectWithParserException()
{
- final IParser<String[]> parser = new DefaultParser<String[]>()
- {
- //
- // DefaultReaderParser
- //
-
- @Override
- protected final String[] createObject(final String[] tokens) throws ParserException
- {
- throw new ParserException("");
- }
- };
+ final IParser<String[], String> parser =
+ new DefaultParser<String[], String>(new DefaultLineTokenizer())
+ {
+ //
+ // DefaultReaderParser
+ //
+
+ @Override
+ protected final String[] createObject(final String[] tokens)
+ throws ParserException
+ {
+ throw new ParserException("");
+ }
+ };
parser.setObjectFactory(IParserObjectFactory.STRING_ARRAY_OBJECT_FACTORY);
try
{
@@ -175,9 +177,9 @@ public final class DefaultParserTest
}
}
- private Iterator<Line> createLineIterator(final List<String> lines)
+ private Iterator<ILine<String>> createLineIterator(final List<String> lines)
{
- return new Iterator<Line>()
+ return new Iterator<ILine<String>>()
{
private final Iterator<String> iterator = lines.iterator();
@@ -188,7 +190,7 @@ public final class DefaultParserTest
throw new UnsupportedOperationException();
}
- public Line next()
+ public ILine<String> next()
{
return new Line(++lineNumber, iterator.next());
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/HeaderLineFilterTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/HeaderLineFilterTest.java
index dd5103f7b36..7c4eb1280ae 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/HeaderLineFilterTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/HeaderLineFilterTest.java
@@ -33,7 +33,7 @@ public class HeaderLineFilterTest
final HeaderLineFilter filter = new HeaderLineFilter();
for (int i = 0; i < 4; ++i)
{
- assert filter.acceptLine("text", i) : "Line " + i;
+ assert filter.acceptLine(new Line(i, "text")) : "Line " + i;
}
}
@@ -56,12 +56,12 @@ public class HeaderLineFilterTest
{
if (headerLine == i)
{
- assert filter.acceptLine("text", i) == false : "Line " + i + " (header line: "
- + headerLine + ")";
+ assert filter.acceptLine(new Line(i, "text")) == false : "Line " + i
+ + " (header line: " + headerLine + ")";
} else
{
- assert filter.acceptLine("text", i) : "Line " + i + " (header line: " + headerLine
- + ")";
+ assert filter.acceptLine(new Line(i, "text")) : "Line " + i + " (header line: "
+ + headerLine + ")";
}
}
}
@@ -70,36 +70,36 @@ public class HeaderLineFilterTest
public void testEmptyHeaderLine()
{
final HeaderLineFilter filter = new HeaderLineFilter(0);
- assert filter.acceptLine("", 0) == false;
- assert filter.acceptLine("something", 1);
+ assert filter.acceptLine(new Line(0, "")) == false;
+ assert filter.acceptLine(new Line(1, "something"));
}
@Test
public void testSkipEmptyLine()
{
final HeaderLineFilter filter = new HeaderLineFilter();
- assert filter.acceptLine("", 0) == false;
+ assert filter.acceptLine(new Line(0, "")) == false;
}
@Test
public void testSkipBlankLine()
{
final HeaderLineFilter filter = new HeaderLineFilter();
- assert filter.acceptLine(" ", 0) == false;
+ assert filter.acceptLine(new Line(0, " ")) == false;
}
@Test
public void testSkipCommentLine()
{
final HeaderLineFilter filter = new HeaderLineFilter();
- assert filter.acceptLine("# Some comment", 0) == false;
+ assert filter.acceptLine(new Line(0, "# Some comment")) == false;
}
@Test
public void testSkipCommentLineWithLeadingWhiteSpace()
{
final HeaderLineFilter filter = new HeaderLineFilter();
- assert filter.acceptLine("\t# Some comment", 0) == false;
+ assert filter.acceptLine(new Line(0, "\t# Some comment")) == false;
}
}
diff --git a/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java b/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
index d4f948377f0..461ea7cefa2 100644
--- a/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
+++ b/common/sourceTest/java/ch/systemsx/cisd/common/parser/ParserUtilitiesTest.java
@@ -43,11 +43,11 @@ import ch.systemsx.cisd.common.parser.filter.NonEmptyLineFilter;
public final class ParserUtilitiesTest
{
- private static final File unitTestRootDirectory =
- new File("targets" + File.separator + "unit-test-wd");
+ private static final File unitTestRootDirectory = new File("targets" + File.separator
+ + "unit-test-wd");
- private static final File workingDirectory =
- new File(unitTestRootDirectory, "ParserUtilitiesTest");
+ private static final File workingDirectory = new File(unitTestRootDirectory,
+ "ParserUtilitiesTest");
@BeforeClass
public final void setUp()
@@ -97,7 +97,7 @@ public final class ParserUtilitiesTest
{ StringUtils.EMPTY, "non-empty line", StringUtils.EMPTY, "hello" };
File file = new File(workingDirectory, "test.txt");
FileUtils.writeLines(file, Arrays.asList(lines));
- Line line = ParserUtilities.tryGetFirstAcceptedLine(file, null);
+ ILine<String> line = ParserUtilities.tryGetFirstAcceptedLine(file, null);
assertEquals(StringUtils.EMPTY, line.getText());
assertEquals(0, line.getNumber());
assert file.delete();
@@ -112,7 +112,7 @@ public final class ParserUtilitiesTest
FileUtils.writeLines(file, Arrays.asList(lines));
ParserUtilities.LineSplitter splitter =
new ParserUtilities.LineSplitter(file, NonEmptyLineFilter.INSTANCE);
- Line line = splitter.tryNextLine();
+ ILine<String> line = splitter.tryNextLine();
assertEquals("non-empty line", line.getText());
assertEquals(1, line.getNumber());
line = splitter.tryNextLine();
@@ -129,7 +129,7 @@ public final class ParserUtilitiesTest
{ StringUtils.EMPTY, "# comment line", StringUtils.EMPTY, "hello" };
File file = new File(workingDirectory, "test.txt");
FileUtils.writeLines(file, Arrays.asList(lines));
- Line line =
+ ILine<String> line =
ParserUtilities.tryGetFirstAcceptedLine(file,
ExcludeEmptyAndCommentLineFilter.INSTANCE);
assertEquals("hello", line.getText());
diff --git a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/java/MigrationStepExecutor.java b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/java/MigrationStepExecutor.java
index c86915657ca..97445fe63d0 100644
--- a/dbmigration/source/java/ch/systemsx/cisd/dbmigration/java/MigrationStepExecutor.java
+++ b/dbmigration/source/java/ch/systemsx/cisd/dbmigration/java/MigrationStepExecutor.java
@@ -24,7 +24,7 @@ import ch.systemsx.cisd.base.exceptions.CheckedExceptionTunnel;
import ch.systemsx.cisd.common.Script;
import ch.systemsx.cisd.common.logging.LogCategory;
import ch.systemsx.cisd.common.logging.LogFactory;
-import ch.systemsx.cisd.common.parser.Line;
+import ch.systemsx.cisd.common.parser.ILine;
import ch.systemsx.cisd.common.parser.ParserUtilities;
import ch.systemsx.cisd.common.parser.filter.ILineFilter;
import ch.systemsx.cisd.common.utilities.ClassUtils;
@@ -79,13 +79,15 @@ public class MigrationStepExecutor extends SimpleJdbcDaoSupport implements IMigr
final ParserUtilities.LineSplitter splitter =
new ParserUtilities.LineSplitter(content, new ILineFilter()
{
- public boolean acceptLine(String line, int lineNumber)
+ public <T> boolean acceptLine(ILine<T> line)
{
- return StringUtils.isNotBlank(line) && line.startsWith("--");
+ String text = line.getText();
+ return StringUtils.isNotBlank(text) && text.startsWith("--");
}
+
});
IMigrationStep stepOrNull = null;
- Line lineOrNull;
+ ILine<?> lineOrNull;
while (stepOrNull == null && (lineOrNull = splitter.tryNextLine()) != null)
{
stepOrNull = tryExtractMigrationStepFromLine(lineOrNull.getText());
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisExcelFileLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisExcelFileLoader.java
new file mode 100644
index 00000000000..56556fce0f7
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/BisExcelFileLoader.java
@@ -0,0 +1,109 @@
+/*
+ * Copyright 2007 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.generic.shared.parser;
+
+import java.util.List;
+import java.util.Map;
+
+import org.apache.poi.ss.usermodel.Sheet;
+
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.io.NamedReader;
+import ch.systemsx.cisd.common.parser.ExcelFileLoader;
+import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
+import ch.systemsx.cisd.common.parser.ParserException;
+import ch.systemsx.cisd.common.parser.ParsingException;
+import ch.systemsx.cisd.common.parser.TabFileLoader;
+
+/**
+ * A <i>openBIS</i> {@link TabFileLoader} extension which translates a {@link ParsingException} into
+ * a more user friendly {@link UserFailureException}.
+ * <p>
+ * Note that this extension prefers to work with {@link NamedReader}.
+ * </p>
+ *
+ * @author Christian Ribeaud
+ */
+public final class BisExcelFileLoader<T> extends ExcelFileLoader<T>
+{
+
+ private static final String MESSAGE_FORMAT =
+ "A problem has occurred while parsing line %d of file '%s':\n %s";
+
+ private static final String ERROR_IN_FILE_MESSAGE_FORMAT =
+ "A problem has occurred while parsing file '%s':\n %s";
+
+ private final boolean acceptEmptyFiles;
+
+ public BisExcelFileLoader(final IParserObjectFactoryFactory<T> factory, boolean acceptEmptyFiles)
+ {
+ super(factory);
+ this.acceptEmptyFiles = acceptEmptyFiles;
+ }
+
+ private final static void translateParsingException(final ParsingException parsingException,
+ final String sectionName)
+ {
+ final RuntimeException causeException = parsingException.getCauseRuntimeException();
+ final String message =
+ causeException == null ? parsingException.getMessage() : causeException
+ .getMessage();
+ throw UserFailureException.fromTemplate(MESSAGE_FORMAT, parsingException.getLineNumber(),
+ sectionName, message);
+ }
+
+ private final static void translateParserException(final ParserException ex,
+ final String sectionName)
+ {
+ final String message = ex.getMessage();
+ throw UserFailureException.fromTemplate(ERROR_IN_FILE_MESSAGE_FORMAT, sectionName, message);
+ }
+
+ //
+ // TabFileLoader
+ //
+ public List<T> load(final Sheet sheet, int begin, int end, String sectionName,
+ final Map<String, String> defaults) throws ParserException, ParsingException,
+ IllegalArgumentException
+ {
+ assert sheet != null : "Excel Sheet cannot be null.";
+ try
+ {
+ final List<T> list = super.load(sheet, begin, end, defaults);
+ if (acceptEmptyFiles == false && list.size() == 0)
+ {
+ throw new UserFailureException("Given file '" + sectionName
+ + "' is empty or does not contain any meaningful information.");
+ }
+ return list;
+ } catch (final IllegalArgumentException illegalArgumentException)
+ {
+ throw new UserFailureException(illegalArgumentException.getMessage(),
+ illegalArgumentException);
+ } catch (final ParsingException e)
+ {
+ translateParsingException(e, sectionName);
+ // Never used.
+ return null;
+ } catch (final ParserException e)
+ {
+ translateParserException(e, sectionName);
+ // Never used.
+ return null;
+ }
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/ExcelFileSection.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/ExcelFileSection.java
new file mode 100644
index 00000000000..dd4a7c33c0b
--- /dev/null
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/ExcelFileSection.java
@@ -0,0 +1,167 @@
+/*
+ * Copyright 2011 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.generic.shared.parser;
+
+import java.io.IOException;
+import java.io.InputStream;
+import java.util.ArrayList;
+import java.util.List;
+
+import org.apache.commons.io.IOUtils;
+import org.apache.poi.hssf.usermodel.HSSFWorkbook;
+import org.apache.poi.poifs.filesystem.POIFSFileSystem;
+import org.apache.poi.ss.usermodel.Cell;
+import org.apache.poi.ss.usermodel.Row;
+import org.apache.poi.ss.usermodel.Sheet;
+import org.apache.poi.ss.usermodel.Workbook;
+
+import ch.systemsx.cisd.base.exceptions.IOExceptionUnchecked;
+import ch.systemsx.cisd.common.exceptions.UserFailureException;
+
+/**
+ * @author Pawel Glyzewski
+ */
+public class ExcelFileSection
+{
+ private static final String SECTION_FILE_DEFAULT = "DEFAULT";
+
+ private final Sheet sheet;
+
+ private final int begin;
+
+ private final int end;
+
+ private final String sectionName;
+
+ private ExcelFileSection(Sheet sheet, String sectionName, int begin, int end)
+ {
+ assert sheet != null;
+ this.sectionName = sectionName;
+ this.sheet = sheet;
+ this.begin = begin;
+ this.end = end;
+ }
+
+ public String getSectionName()
+ {
+ return sectionName;
+ }
+
+ public Sheet getSheet()
+ {
+ return sheet;
+ }
+
+ public int getBegin()
+ {
+ return begin;
+ }
+
+ public int getEnd()
+ {
+ return end;
+ }
+
+ public static ExcelFileSection createFromInputStream(InputStream stream, String sectionName)
+ {
+ try
+ {
+ POIFSFileSystem poifsFileSystem = new POIFSFileSystem(stream);
+ Workbook wb = new HSSFWorkbook(poifsFileSystem);
+ Sheet sheet = wb.getSheetAt(0);
+ return new ExcelFileSection(sheet, sectionName, 0, sheet.getLastRowNum());
+ } catch (IOException e)
+ {
+ throw new IOExceptionUnchecked(e);
+ }
+ }
+
+ public static List<ExcelFileSection> extractSections(InputStream stream)
+ {
+ List<ExcelFileSection> sections = new ArrayList<ExcelFileSection>();
+ try
+ {
+ POIFSFileSystem poifsFileSystem = new POIFSFileSystem(stream);
+ Workbook wb = new HSSFWorkbook(poifsFileSystem);
+ Sheet sheet = wb.getSheetAt(0);
+ String sectionName = null;
+ Integer begin = null;
+ for (Row row : sheet)
+ {
+ String newSectionName = tryGetSectionName(row);
+ if (newSectionName != null)
+ {
+ if (sectionName != null && begin != null)
+ {
+ if (sectionName.equals(newSectionName))
+ {
+ continue;
+ }
+ if (newSectionName.equals(SECTION_FILE_DEFAULT))
+ {
+ continue;
+ } else
+ {
+ sections.add(new ExcelFileSection(sheet, sectionName, begin, row
+ .getRowNum()));
+ sectionName = newSectionName;
+ begin = row.getRowNum() + 1;
+ }
+ } else
+ {
+ sectionName = newSectionName;
+ begin = row.getRowNum() + 1;
+ }
+ } else if (sectionName == null || begin == null)
+ {
+ throw new UserFailureException("Discovered the unnamed section in the file");
+ }
+ if (row.getRowNum() == sheet.getLastRowNum())
+ {
+ sections.add(new ExcelFileSection(sheet, sectionName, begin, row.getRowNum()));
+ }
+ }
+ } catch (IOException e)
+ {
+ throw new IOExceptionUnchecked(e);
+ } finally
+ {
+ IOUtils.closeQuietly(stream);
+ }
+ return sections;
+ }
+
+ private static String tryGetSectionName(Row row)
+ {
+ final String beginSection = "[";
+ final String endSection = "]";
+ if (row == null || row.getCell(0) == null
+ || row.getCell(0).getCellType() != Cell.CELL_TYPE_STRING)
+ {
+ return null;
+ }
+ String trimmedCell = row.getCell(0).getStringCellValue();
+
+ if (trimmedCell.startsWith(beginSection) && trimmedCell.endsWith(endSection))
+ {
+ return trimmedCell.substring(1, trimmedCell.length() - 1);
+ } else
+ {
+ return null;
+ }
+ }
+}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
index e343d31ed4b..a7ca423d9e4 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/SampleUploadSectionsParser.java
@@ -24,6 +24,7 @@ import java.util.List;
import java.util.Map;
import ch.systemsx.cisd.common.io.DelegatedReader;
+import ch.systemsx.cisd.common.parser.ExcelFileLoader;
import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
@@ -153,6 +154,34 @@ public class SampleUploadSectionsParser
return tabFileLoader;
}
+ private static BisExcelFileLoader<NewSample> createSampleLoaderFromExcel(
+ final SampleType sampleType, final boolean isAutoGenerateCodes,
+ final boolean allowExperiments, final BatchOperationKind operationKind)
+ {
+ final BisExcelFileLoader<NewSample> tabFileLoader =
+ new BisExcelFileLoader<NewSample>(new IParserObjectFactoryFactory<NewSample>()
+ {
+ public final IParserObjectFactory<NewSample> createFactory(
+ final IPropertyMapper propertyMapper) throws ParserException
+ {
+ switch (operationKind)
+ {
+ case REGISTRATION:
+ return new NewSampleParserObjectFactory(sampleType,
+ propertyMapper, isAutoGenerateCodes == false,
+ allowExperiments);
+ case UPDATE:
+ return new UpdatedSampleParserObjectFactory(sampleType,
+ propertyMapper, isAutoGenerateCodes == false,
+ allowExperiments);
+ }
+ throw new UnsupportedOperationException(operationKind
+ + " is not supported");
+ }
+ }, true);
+ return tabFileLoader;
+ }
+
private static List<BatchRegistrationResult> loadSamplesFromFiles(
Collection<NamedInputStream> uploadedFiles, SampleType sampleType,
boolean isAutoGenerateCodes, final List<NewSamplesWithTypes> newSamples,
@@ -162,50 +191,98 @@ public class SampleUploadSectionsParser
new ArrayList<BatchRegistrationResult>(uploadedFiles.size());
for (final NamedInputStream multipartFile : uploadedFiles)
{
- List<FileSection> sampleSections = new ArrayList<FileSection>();
- if (sampleType.isDefinedInFileEntityTypeCode())
+ if (multipartFile.getOriginalFilename().toLowerCase().endsWith("xls"))
{
- sampleSections
- .addAll(FileSection.extractSections(multipartFile.getUnicodeReader()));
+ List<ExcelFileSection> sampleSections = new ArrayList<ExcelFileSection>();
+ if (sampleType.isDefinedInFileEntityTypeCode())
+ {
+ sampleSections.addAll(ExcelFileSection.extractSections(multipartFile
+ .getInputStream()));
+ } else
+ {
+ sampleSections.add(ExcelFileSection.createFromInputStream(
+ multipartFile.getInputStream(), sampleType.getCode()));
+ }
+ int sampleCounter = 0;
+ Map<String, String> defaults = Collections.emptyMap();
+ for (ExcelFileSection fs : sampleSections)
+ {
+ if (fs.getSectionName().equals("DEFAULT"))
+ {
+ defaults =
+ Collections.unmodifiableMap(ExcelFileLoader.parseDefaults(
+ fs.getSheet(), fs.getBegin(), fs.getEnd()));
+ } else
+ {
+ SampleType typeFromSection = new SampleType();
+ typeFromSection.setCode(fs.getSectionName());
+ final BisExcelFileLoader<NewSample> excelFileLoader =
+ createSampleLoaderFromExcel(typeFromSection, isAutoGenerateCodes,
+ allowExperiments, operationKind);
+ String sectionInFile =
+ sampleSections.size() == 1 ? "" : " (section:"
+ + fs.getSectionName() + ")";
+ final List<NewSample> loadedSamples =
+ excelFileLoader.load(fs.getSheet(), fs.getBegin(), fs.getEnd(),
+ multipartFile.getOriginalFilename() + sectionInFile,
+ defaults);
+ if (loadedSamples.size() > 0)
+ {
+ newSamples.add(new NewSamplesWithTypes(typeFromSection, loadedSamples));
+ sampleCounter += loadedSamples.size();
+ }
+ }
+ }
+ results.add(new BatchRegistrationResult(multipartFile.getOriginalFilename(), String
+ .format("%s of %d sample(s) is complete.", operationKind.getDescription(),
+ sampleCounter)));
} else
{
- sampleSections.add(FileSection.createFromInputStream(
- multipartFile.getInputStream(), sampleType.getCode()));
- }
- int sampleCounter = 0;
- Map<String, String> defaults = Collections.emptyMap();
- for (FileSection fs : sampleSections)
- {
- if (fs.getSectionName().equals("DEFAULT"))
+ List<FileSection> sampleSections = new ArrayList<FileSection>();
+ if (sampleType.isDefinedInFileEntityTypeCode())
{
- defaults =
- Collections.unmodifiableMap(TabFileLoader.parseDefaults(fs
- .getContentReader()));
+ sampleSections.addAll(FileSection.extractSections(multipartFile
+ .getUnicodeReader()));
} else
{
- Reader reader = fs.getContentReader();
- SampleType typeFromSection = new SampleType();
- typeFromSection.setCode(fs.getSectionName());
- final BisTabFileLoader<NewSample> tabFileLoader =
- createSampleLoader(typeFromSection, isAutoGenerateCodes,
- allowExperiments, operationKind);
- String sectionInFile =
- sampleSections.size() == 1 ? "" : " (section:" + fs.getSectionName()
- + ")";
- final List<NewSample> loadedSamples =
- tabFileLoader.load(
- new DelegatedReader(reader, multipartFile.getOriginalFilename()
- + sectionInFile), defaults);
- if (loadedSamples.size() > 0)
+ sampleSections.add(FileSection.createFromInputStream(
+ multipartFile.getInputStream(), sampleType.getCode()));
+ }
+ int sampleCounter = 0;
+ Map<String, String> defaults = Collections.emptyMap();
+ for (FileSection fs : sampleSections)
+ {
+ if (fs.getSectionName().equals("DEFAULT"))
+ {
+ defaults =
+ Collections.unmodifiableMap(TabFileLoader.parseDefaults(fs
+ .getContentReader()));
+ } else
{
- newSamples.add(new NewSamplesWithTypes(typeFromSection, loadedSamples));
- sampleCounter += loadedSamples.size();
+ Reader reader = fs.getContentReader();
+ SampleType typeFromSection = new SampleType();
+ typeFromSection.setCode(fs.getSectionName());
+ final BisTabFileLoader<NewSample> tabFileLoader =
+ createSampleLoader(typeFromSection, isAutoGenerateCodes,
+ allowExperiments, operationKind);
+ String sectionInFile =
+ sampleSections.size() == 1 ? "" : " (section:"
+ + fs.getSectionName() + ")";
+ final List<NewSample> loadedSamples =
+ tabFileLoader.load(
+ new DelegatedReader(reader, multipartFile
+ .getOriginalFilename() + sectionInFile), defaults);
+ if (loadedSamples.size() > 0)
+ {
+ newSamples.add(new NewSamplesWithTypes(typeFromSection, loadedSamples));
+ sampleCounter += loadedSamples.size();
+ }
}
}
+ results.add(new BatchRegistrationResult(multipartFile.getOriginalFilename(), String
+ .format("%s of %d sample(s) is complete.", operationKind.getDescription(),
+ sampleCounter)));
}
- results.add(new BatchRegistrationResult(multipartFile.getOriginalFilename(), String
- .format("%s of %d sample(s) is complete.", operationKind.getDescription(),
- sampleCounter)));
}
return results;
}
@@ -249,5 +326,4 @@ public class SampleUploadSectionsParser
}
}
}
-
}
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/MaterialUploadSectionsParser.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/MaterialUploadSectionsParser.java
index 8c1fdd629d9..678bdbd2152 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/MaterialUploadSectionsParser.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/parser/MaterialUploadSectionsParser.java
@@ -24,6 +24,7 @@ import java.util.List;
import java.util.Map;
import ch.systemsx.cisd.common.io.DelegatedReader;
+import ch.systemsx.cisd.common.parser.ExcelFileLoader;
import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
@@ -33,7 +34,9 @@ import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.MaterialType;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterialsWithTypes;
+import ch.systemsx.cisd.openbis.generic.shared.parser.BisExcelFileLoader;
import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
+import ch.systemsx.cisd.openbis.generic.shared.parser.ExcelFileSection;
import ch.systemsx.cisd.openbis.generic.shared.parser.FileSection;
import ch.systemsx.cisd.openbis.generic.shared.parser.NamedInputStream;
@@ -105,59 +108,117 @@ public class MaterialUploadSectionsParser
new ArrayList<BatchRegistrationResult>(uploadedFiles.size());
for (final NamedInputStream multipartFile : uploadedFiles)
{
- List<FileSection> materialSections = new ArrayList<FileSection>();
- if (materialType.isDefinedInFileEntityTypeCode())
+ if (multipartFile.getOriginalFilename().toLowerCase().endsWith("xls"))
{
- materialSections.addAll(FileSection.extractSections(multipartFile
- .getUnicodeReader()));
+ List<ExcelFileSection> materialSections = new ArrayList<ExcelFileSection>();
+ if (materialType.isDefinedInFileEntityTypeCode())
+ {
+ materialSections.addAll(ExcelFileSection.extractSections(multipartFile
+ .getInputStream()));
+ } else
+ {
+ materialSections.add(ExcelFileSection.createFromInputStream(
+ multipartFile.getInputStream(), materialType.getCode()));
+ }
+ int materialCounter = 0;
+ Map<String, String> defaults = Collections.emptyMap();
+ for (ExcelFileSection fs : materialSections)
+ {
+ if (fs.getSectionName().equals("DEFAULT"))
+ {
+ defaults =
+ Collections.unmodifiableMap(ExcelFileLoader.parseDefaults(
+ fs.getSheet(), fs.getBegin(), fs.getEnd()));
+ } else
+ {
+ MaterialType typeFromSection = new MaterialType();
+ typeFromSection.setCode(fs.getSectionName());
+ final BisExcelFileLoader<NewMaterial> excelFileLoader =
+ new BisExcelFileLoader<NewMaterial>(
+ new IParserObjectFactoryFactory<NewMaterial>()
+ {
+ public final IParserObjectFactory<NewMaterial> createFactory(
+ final IPropertyMapper propertyMapper)
+ throws ParserException
+ {
+ return new NewMaterialParserObjectFactory(
+ propertyMapper);
+ }
+ }, false);
+ String sectionInFile =
+ materialSections.size() == 1 ? "" : " (section:"
+ + fs.getSectionName() + ")";
+ final List<NewMaterial> loadedMaterials =
+ excelFileLoader.load(fs.getSheet(), fs.getBegin(), fs.getEnd(),
+ multipartFile.getOriginalFilename() + sectionInFile,
+ defaults);
+ if (loadedMaterials.size() > 0)
+ {
+ newMaterials.add(new NewMaterialsWithTypes(typeFromSection,
+ loadedMaterials));
+ materialCounter += loadedMaterials.size();
+ }
+ }
+ }
+ results.add(new BatchRegistrationResult(multipartFile.getOriginalFilename(), String
+ .format("Registration of %d material(s) is complete.", materialCounter)));
} else
{
- materialSections.add(FileSection.createFromInputStream(
- multipartFile.getInputStream(), materialType.getCode()));
- }
- int materialCounter = 0;
- Map<String, String> defaults = Collections.emptyMap();
- for (FileSection fs : materialSections)
- {
- if (fs.getSectionName().equals("DEFAULT"))
+
+ List<FileSection> materialSections = new ArrayList<FileSection>();
+ if (materialType.isDefinedInFileEntityTypeCode())
{
- defaults =
- Collections.unmodifiableMap(TabFileLoader.parseDefaults(fs
- .getContentReader()));
+ materialSections.addAll(FileSection.extractSections(multipartFile
+ .getUnicodeReader()));
} else
{
- Reader reader = fs.getContentReader();
- MaterialType typeFromSection = new MaterialType();
- typeFromSection.setCode(fs.getSectionName());
- BisTabFileLoader<NewMaterial> tabFileLoader =
- new BisTabFileLoader<NewMaterial>(
- new IParserObjectFactoryFactory<NewMaterial>()
- {
- public final IParserObjectFactory<NewMaterial> createFactory(
- final IPropertyMapper propertyMapper)
- throws ParserException
- {
- return new NewMaterialParserObjectFactory(
- propertyMapper);
- }
- }, false);
- String sectionInFile =
- materialSections.size() == 1 ? "" : " (section:" + fs.getSectionName()
- + ")";
- final List<NewMaterial> loadedMaterials =
- tabFileLoader.load(
- new DelegatedReader(reader, multipartFile.getOriginalFilename()
- + sectionInFile), defaults);
- if (loadedMaterials.size() > 0)
+ materialSections.add(FileSection.createFromInputStream(
+ multipartFile.getInputStream(), materialType.getCode()));
+ }
+ int materialCounter = 0;
+ Map<String, String> defaults = Collections.emptyMap();
+ for (FileSection fs : materialSections)
+ {
+ if (fs.getSectionName().equals("DEFAULT"))
{
- newMaterials
- .add(new NewMaterialsWithTypes(typeFromSection, loadedMaterials));
- materialCounter += loadedMaterials.size();
+ defaults =
+ Collections.unmodifiableMap(TabFileLoader.parseDefaults(fs
+ .getContentReader()));
+ } else
+ {
+ Reader reader = fs.getContentReader();
+ MaterialType typeFromSection = new MaterialType();
+ typeFromSection.setCode(fs.getSectionName());
+ BisTabFileLoader<NewMaterial> tabFileLoader =
+ new BisTabFileLoader<NewMaterial>(
+ new IParserObjectFactoryFactory<NewMaterial>()
+ {
+ public final IParserObjectFactory<NewMaterial> createFactory(
+ final IPropertyMapper propertyMapper)
+ throws ParserException
+ {
+ return new NewMaterialParserObjectFactory(
+ propertyMapper);
+ }
+ }, false);
+ String sectionInFile =
+ materialSections.size() == 1 ? "" : " (section:"
+ + fs.getSectionName() + ")";
+ final List<NewMaterial> loadedMaterials =
+ tabFileLoader.load(
+ new DelegatedReader(reader, multipartFile
+ .getOriginalFilename() + sectionInFile), defaults);
+ if (loadedMaterials.size() > 0)
+ {
+ newMaterials.add(new NewMaterialsWithTypes(typeFromSection,
+ loadedMaterials));
+ materialCounter += loadedMaterials.size();
+ }
}
}
+ results.add(new BatchRegistrationResult(multipartFile.getOriginalFilename(), String
+ .format("Registration of %d material(s) is complete.", materialCounter)));
}
- results.add(new BatchRegistrationResult(multipartFile.getOriginalFilename(), String
- .format("Registration of %d material(s) is complete.", materialCounter)));
}
return results;
}
--
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