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
index 1f81c132aa134034f6395e1a1e343319a81ebc22..9e9c052d2f8fd6b00f989620ab65c4c1d0fc3e7a 100644
--- 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
@@ -19,6 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.io.IOException;
import java.io.InputStream;
import java.util.ArrayList;
+import java.util.LinkedList;
import java.util.List;
import org.apache.commons.io.IOUtils;
@@ -104,77 +105,115 @@ public class ExcelFileSection
}
}
+ public static List<ExcelFileSection> extractSectionsFromWorkBook(Workbook wb,
+ String excelSheetName)
+ {
+ LinkedList<ExcelFileSection> sections = new LinkedList<ExcelFileSection>();
+ List<ExcelFileSection> defaultSheetSections = null;
+
+ Sheet sheet = null;
+ String prefix = excelSheetName + "-";
+ for (int i = 0; i < wb.getNumberOfSheets(); i++)
+ {
+ String sheetName = wb.getSheetName(i);
+ if (excelSheetName.equalsIgnoreCase(sheetName))
+ {
+ sheet = wb.getSheetAt(i);
+ defaultSheetSections = extractSectionsFromDefaultSheet(sheet);
+ } else if (sheetName.startsWith(prefix))
+ {
+ String sectionName = sheetName.substring(prefix.length());
+ sheet = wb.getSheetAt(i);
+ if (SECTION_FILE_DEFAULT.equalsIgnoreCase(sectionName))
+ {
+ sections.addFirst(new ExcelFileSection(sheet, sectionName, 0, sheet
+ .getLastRowNum()));
+ } else
+ {
+ sections.add(new ExcelFileSection(sheet, sectionName, 0, sheet.getLastRowNum()));
+ }
+ }
+ }
+
+ // default sheet sections must be at the end of the file
+ if (defaultSheetSections != null)
+ {
+ sections.addAll(defaultSheetSections);
+ }
+
+ return sections;
+ }
+
public static List<ExcelFileSection> extractSections(InputStream stream, String excelSheetName,
String fileName)
{
- List<ExcelFileSection> sections = new ArrayList<ExcelFileSection>();
try
{
Workbook wb = getWorkBook(stream, fileName);
- Sheet sheet = null;
if (excelSheetName == null)
{
- sheet = wb.getSheetAt(0);
+ return extractSectionsFromDefaultSheet(wb.getSheetAt(0));
} else
{
- for (int i = 0; i < wb.getNumberOfSheets(); i++)
- {
- if (excelSheetName.equalsIgnoreCase(wb.getSheetName(i)))
- {
- sheet = wb.getSheetAt(i);
- break;
- }
- }
- if (sheet == null)
- {
- return sections;
- }
+ return extractSectionsFromWorkBook(wb, excelSheetName);
}
- String sectionName = null;
- Integer begin = null;
- for (Row row : sheet)
+ } catch (IOException e)
+ {
+ throw new IOExceptionUnchecked(e);
+ } finally
+ {
+ IOUtils.closeQuietly(stream);
+ }
+ }
+
+ private static final List<ExcelFileSection> extractSectionsFromDefaultSheet(Sheet sheet)
+ {
+ List<ExcelFileSection> sections = new ArrayList<ExcelFileSection>();
+
+ if (sheet == null)
+ {
+ return sections;
+ }
+
+ String sectionName = null;
+ Integer begin = null;
+ for (Row row : sheet)
+ {
+ String newSectionName = tryGetSectionName(row);
+ if (newSectionName != null)
{
- String newSectionName = tryGetSectionName(row);
- if (newSectionName != null)
+ if (sectionName != null && begin != null)
{
- if (sectionName != null && begin != null)
+ if (sectionName.equals(newSectionName))
{
- if (sectionName.equals(newSectionName))
- {
- continue;
- }
- if (newSectionName.equals(SECTION_FILE_DEFAULT))
- {
- continue;
- } else
- {
- sections.add(new ExcelFileSection(sheet, sectionName, begin, row
- .getRowNum() - 1));
- sectionName = newSectionName;
- begin = row.getRowNum() + 1;
- }
+ continue;
+ }
+ if (newSectionName.equals(SECTION_FILE_DEFAULT))
+ {
+ continue;
} else
{
+ sections.add(new ExcelFileSection(sheet, sectionName, begin, row
+ .getRowNum() - 1));
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())
+ } else
{
- sections.add(new ExcelFileSection(sheet, sectionName, begin, row.getRowNum()));
+ 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;
}
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 66f5ed50f856a07f108e9e2e6e959b2e0d9dfdcb..cc1c99a61e084191d063df10bdcefd7cb3ad6d4a 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
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.io.Reader;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Collections;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -206,14 +206,13 @@ public class SampleUploadSectionsParser
multipartFile.getInputStream(), sampleType.getCode(), loweredFileName));
}
int sampleCounter = 0;
- Map<String, String> defaults = Collections.emptyMap();
+ Map<String, String> defaults = new HashMap<String, String>();
for (ExcelFileSection fs : sampleSections)
{
if (fs.getSectionName().equals("DEFAULT"))
{
- defaults =
- Collections.unmodifiableMap(ExcelFileLoader.parseDefaults(
- fs.getSheet(), fs.getBegin(), fs.getEnd()));
+ defaults.putAll(ExcelFileLoader.parseDefaults(fs.getSheet(), fs.getBegin(),
+ fs.getEnd()));
} else
{
SampleType typeFromSection = new SampleType();
@@ -250,14 +249,12 @@ public class SampleUploadSectionsParser
multipartFile.getInputStream(), sampleType.getCode()));
}
int sampleCounter = 0;
- Map<String, String> defaults = Collections.emptyMap();
+ Map<String, String> defaults = new HashMap<String, String>();
for (FileSection fs : sampleSections)
{
if (fs.getSectionName().equals("DEFAULT"))
{
- defaults =
- Collections.unmodifiableMap(TabFileLoader.parseDefaults(fs
- .getContentReader()));
+ defaults.putAll(TabFileLoader.parseDefaults(fs.getContentReader()));
} else
{
Reader reader = fs.getContentReader();
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 ad0acf361cce12c6cae5501f91519f0a9775ea6a..7008fe4b90d1ffc92d865c0cfd5812a5eb3bbfdb 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
@@ -19,7 +19,7 @@ package ch.systemsx.cisd.openbis.plugin.generic.client.web.server.parser;
import java.io.Reader;
import java.util.ArrayList;
import java.util.Collection;
-import java.util.Collections;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
@@ -126,14 +126,13 @@ public class MaterialUploadSectionsParser
loweredFileName));
}
int materialCounter = 0;
- Map<String, String> defaults = Collections.emptyMap();
+ Map<String, String> defaults = new HashMap<String, String>();
for (ExcelFileSection fs : materialSections)
{
if (fs.getSectionName().equals("DEFAULT"))
{
- defaults =
- Collections.unmodifiableMap(ExcelFileLoader.parseDefaults(
- fs.getSheet(), fs.getBegin(), fs.getEnd()));
+ defaults.putAll(ExcelFileLoader.parseDefaults(fs.getSheet(), fs.getBegin(),
+ fs.getEnd()));
} else
{
MaterialType typeFromSection = new MaterialType();
@@ -180,14 +179,12 @@ public class MaterialUploadSectionsParser
multipartFile.getInputStream(), materialType.getCode()));
}
int materialCounter = 0;
- Map<String, String> defaults = Collections.emptyMap();
+ Map<String, String> defaults = new HashMap<String, String>();
for (FileSection fs : materialSections)
{
if (fs.getSectionName().equals("DEFAULT"))
{
- defaults =
- Collections.unmodifiableMap(TabFileLoader.parseDefaults(fs
- .getContentReader()));
+ defaults.putAll(TabFileLoader.parseDefaults(fs.getContentReader()));
} else
{
Reader reader = fs.getContentReader();