From ad570809aac451390d58617062a0e95000ec8a5c Mon Sep 17 00:00:00 2001
From: buczekp <buczekp>
Date: Mon, 6 Dec 2010 17:09:13 +0000
Subject: [PATCH] [LMS-1907] refactorization: simplify NamedInputStream (no
need to work on byte array); fixed encoding in upload of library
SVN: 19018
---
.../cisd/common/utilities/UnicodeUtils.java | 7 ++
.../shared/parser/NamedInputStream.java | 20 ++--
.../parser/SampleUploadSectionsParser.java | 94 +++++++++++--------
.../client/web/server/DataSetLoader.java | 3 +-
.../client/web/server/ExperimentLoader.java | 3 +-
.../web/server/GenericClientService.java | 15 +--
.../client/web/server/MaterialLoader.java | 3 +-
.../web/server/UpdatedExperimentLoader.java | 3 +-
.../client/web/server/LibraryExtractor.java | 5 +-
.../LibraryEntityRegistrator.java | 4 +-
.../ScreeningLibraryTransformer.java | 16 +++-
11 files changed, 98 insertions(+), 75 deletions(-)
diff --git a/common/source/java/ch/systemsx/cisd/common/utilities/UnicodeUtils.java b/common/source/java/ch/systemsx/cisd/common/utilities/UnicodeUtils.java
index 5bf5236b4ad..27cedb5aa70 100644
--- a/common/source/java/ch/systemsx/cisd/common/utilities/UnicodeUtils.java
+++ b/common/source/java/ch/systemsx/cisd/common/utilities/UnicodeUtils.java
@@ -20,6 +20,7 @@ import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.Reader;
import java.io.UnsupportedEncodingException;
+import java.nio.charset.Charset;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
@@ -38,6 +39,12 @@ public final class UnicodeUtils
// Can not be instantiated.
}
+ /** @returns {@link Charset} for {@link #DEFAULT_UNICODE_CHARSET} */
+ public final static Charset getDefaultUnicodeCharset()
+ {
+ return Charset.forName(UnicodeUtils.DEFAULT_UNICODE_CHARSET);
+ }
+
/**
* @return {@link Reader} that uses the default Unicode encoding.
* @throws EnvironmentFailureException if the encoding is not supported (shouldn't happen).
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NamedInputStream.java b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NamedInputStream.java
index 5556981bdb0..23c90fd4610 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NamedInputStream.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/generic/shared/parser/NamedInputStream.java
@@ -17,11 +17,13 @@
package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.io.InputStream;
+import java.io.Reader;
-import org.springframework.web.multipart.MultipartFile;
+import ch.systemsx.cisd.common.utilities.UnicodeUtils;
/**
* @author Izabela Adamczyk
+ * @author Piotr Buczek
*/
public class NamedInputStream
{
@@ -30,15 +32,15 @@ public class NamedInputStream
private final String originalName;
- private final byte[] bytes;
-
- public NamedInputStream(InputStream stream, String originalName, byte[] bytes)
+ public NamedInputStream(InputStream stream, String originalName)
{
this.stream = stream;
this.originalName = originalName;
- this.bytes = bytes;
}
+ /**
+ * NOTE: use {@link #getUnicodeReader()} to get Unicode characters.
+ */
public InputStream getInputStream()
{
return stream;
@@ -50,10 +52,12 @@ public class NamedInputStream
}
/**
- * @see MultipartFile#getBytes()
+ * @return Reader of unicode characters from this input stream
+ * <p>
+ * Use {@link #getInputStream()} instead to get raw input stream.
*/
- public byte[] getBytes()
+ public Reader getUnicodeReader()
{
- return bytes;
+ return UnicodeUtils.createReader(stream);
}
}
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 c96860d8869..4bf7ad36ab8 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 +19,6 @@ package ch.systemsx.cisd.openbis.generic.shared.parser;
import java.io.InputStream;
import java.io.Reader;
import java.io.StringReader;
-import java.io.UnsupportedEncodingException;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
@@ -95,33 +94,27 @@ public class SampleUploadSectionsParser
{
final List<NewSamplesWithTypes> newSamples = new ArrayList<NewSamplesWithTypes>();
boolean isAutoGenerateCodes = (sampleCodeGeneratorOrNull != null);
- try
- {
- final List<BatchRegistrationResult> results =
- loadSamplesFromFiles(files, sampleType, isAutoGenerateCodes, newSamples,
- allowExperiments, operationKind);
+ final List<BatchRegistrationResult> results =
+ loadSamplesFromFiles(files, sampleType, isAutoGenerateCodes, newSamples,
+ allowExperiments, operationKind);
- if (defaultGroupIdentifier != null)
+ if (defaultGroupIdentifier != null)
+ {
+ switch (operationKind)
{
- switch (operationKind)
- {
- case REGISTRATION:
- if (isAutoGenerateCodes)
- {
- generateIdentifiers(defaultGroupIdentifier, sampleCodeGeneratorOrNull,
- isAutoGenerateCodes, newSamples);
- }
- break;
- case UPDATE:
- fillIdentifiers(defaultGroupIdentifier, newSamples);
- break;
- }
+ case REGISTRATION:
+ if (isAutoGenerateCodes)
+ {
+ generateIdentifiers(defaultGroupIdentifier, sampleCodeGeneratorOrNull,
+ isAutoGenerateCodes, newSamples);
+ }
+ break;
+ case UPDATE:
+ fillIdentifiers(defaultGroupIdentifier, newSamples);
+ break;
}
- return new BatchSamplesOperation(newSamples, results, parseCodes(newSamples));
- } catch (UnsupportedEncodingException ex)
- {
- throw new UserFailureException(ex.getMessage());
}
+ return new BatchSamplesOperation(newSamples, results, parseCodes(newSamples));
}
private static String[] parseCodes(final List<NewSamplesWithTypes> newSamples)
@@ -167,19 +160,43 @@ public class SampleUploadSectionsParser
static class FileSection
{
- private final String content;
+ private final String contentOrNull;
+
+ private final InputStream contentStreamOrNull;
private final String sectionName;
- public FileSection(String content, String sectionName)
+ // assumption that the given string is encoded using Unicode
+ public static FileSection createFromString(String content, String sectionName)
+ {
+ return new FileSection(content, sectionName, null);
+ }
+
+ public static FileSection createFromInputStream(InputStream contentStream,
+ String sectionName)
{
+ return new FileSection(null, sectionName, contentStream);
+ }
+
+ private FileSection(String contentOrNull, String sectionName,
+ InputStream contentStreamOrNull)
+ {
+ assert (contentOrNull != null && contentStreamOrNull == null)
+ || (contentOrNull == null && contentStreamOrNull != null);
this.sectionName = sectionName;
- this.content = content;
+ this.contentOrNull = contentOrNull;
+ this.contentStreamOrNull = contentStreamOrNull;
}
- public String getContent()
+ public Reader getContentReader()
{
- return content;
+ if (contentOrNull != null)
+ {
+ return new StringReader(contentOrNull);
+ } else
+ {
+ return UnicodeUtils.createReader(contentStreamOrNull);
+ }
}
public String getSectionName()
@@ -188,13 +205,11 @@ public class SampleUploadSectionsParser
}
}
- private static List<FileSection> extractSections(InputStream stream)
+ private static List<FileSection> extractSections(Reader reader)
{
List<FileSection> sections = new ArrayList<FileSection>();
- Reader reader = null;
try
{
- reader = UnicodeUtils.createReader(stream);
LineIterator it = IOUtils.lineIterator(reader);
StringBuilder sb = null;
String sectionName = null;
@@ -206,7 +221,7 @@ public class SampleUploadSectionsParser
{
if (sectionName != null && sb != null)
{
- sections.add(new FileSection(sb.toString(), sectionName));
+ sections.add(FileSection.createFromString(sb.toString(), sectionName));
}
sectionName = newSectionName;
sb = new StringBuilder();
@@ -223,7 +238,7 @@ public class SampleUploadSectionsParser
}
if (it.hasNext() == false)
{
- sections.add(new FileSection(sb.toString(), sectionName));
+ sections.add(FileSection.createFromString(sb.toString(), sectionName));
}
}
} finally
@@ -255,7 +270,6 @@ public class SampleUploadSectionsParser
Collection<NamedInputStream> uploadedFiles, SampleType sampleType,
boolean isAutoGenerateCodes, final List<NewSamplesWithTypes> newSamples,
boolean allowExperiments, BatchOperationKind operationKind)
- throws UnsupportedEncodingException
{
final List<BatchRegistrationResult> results =
new ArrayList<BatchRegistrationResult>(uploadedFiles.size());
@@ -264,16 +278,16 @@ public class SampleUploadSectionsParser
List<FileSection> sampleSections = new ArrayList<FileSection>();
if (sampleType.isDefinedInFileEntityTypeCode())
{
- sampleSections.addAll(extractSections(multipartFile.getInputStream()));
+ sampleSections.addAll(extractSections(multipartFile.getUnicodeReader()));
} else
{
- sampleSections.add(new FileSection(new String(multipartFile.getBytes(),
- UnicodeUtils.DEFAULT_UNICODE_CHARSET), sampleType.getCode()));
+ sampleSections.add(FileSection.createFromInputStream(
+ multipartFile.getInputStream(), sampleType.getCode()));
}
int sampleCounter = 0;
for (FileSection fs : sampleSections)
{
- final StringReader stringReader = new StringReader(fs.getContent());
+ Reader reader = fs.getContentReader();
SampleType typeFromSection = new SampleType();
typeFromSection.setCode(fs.getSectionName());
final BisTabFileLoader<NewSample> tabFileLoader =
@@ -282,7 +296,7 @@ public class SampleUploadSectionsParser
String sectionInFile =
sampleSections.size() == 1 ? "" : " (section:" + fs.getSectionName() + ")";
final List<NewSample> loadedSamples =
- tabFileLoader.load(new DelegatedReader(stringReader, multipartFile
+ tabFileLoader.load(new DelegatedReader(reader, multipartFile
.getOriginalFilename() + sectionInFile));
if (loadedSamples.size() > 0)
{
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/DataSetLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/DataSetLoader.java
index 84427112c89..a53b7407149 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/DataSetLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/DataSetLoader.java
@@ -25,7 +25,6 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.common.utilities.UnicodeUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewDataSet;
import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
@@ -61,7 +60,7 @@ public class DataSetLoader
results = new ArrayList<BatchRegistrationResult>(files.size());
for (final NamedInputStream file : files)
{
- final Reader reader = UnicodeUtils.createReader(file.getInputStream());
+ final Reader reader = file.getUnicodeReader();
final List<NewDataSet> loadedMaterials =
tabFileLoader.load(new DelegatedReader(reader, file.getOriginalFilename()));
newObjects.addAll(loadedMaterials);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentLoader.java
index 23b9e0b945f..e46cb10816a 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/ExperimentLoader.java
@@ -26,7 +26,6 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.common.utilities.UnicodeUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewBasicExperiment;
import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
@@ -64,7 +63,7 @@ public class ExperimentLoader
results = new ArrayList<BatchRegistrationResult>(files.size());
for (final NamedInputStream file : files)
{
- final Reader reader = UnicodeUtils.createReader(file.getInputStream());
+ final Reader reader = file.getUnicodeReader();
final List<NewBasicExperiment> loadedExperiments =
tabFileLoader.load(new DelegatedReader(reader, file.getOriginalFilename()));
newExperiments.addAll(loadedExperiments);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
index 8c19f982985..1c9b8c22812 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/GenericClientService.java
@@ -259,8 +259,7 @@ public class GenericClientService extends AbstractClientService implements IGene
new ArrayList<NamedInputStream>(uploadedFiles.size());
for (IUncheckedMultipartFile f : uploadedFiles.iterable())
{
- files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename(), f
- .getBytes()));
+ files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename()));
}
return SampleUploadSectionsParser.prepareSamples(sampleType, files,
defaultGroupIdentifier, sampleCodeGeneratorOrNull, allowExperiments,
@@ -369,8 +368,7 @@ public class GenericClientService extends AbstractClientService implements IGene
new ArrayList<NamedInputStream>(uploadedFiles.size());
for (IUncheckedMultipartFile f : uploadedFiles.iterable())
{
- files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename(), f
- .getBytes()));
+ files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename()));
}
ExperimentLoader loader = new ExperimentLoader();
loader.load(files);
@@ -392,8 +390,7 @@ public class GenericClientService extends AbstractClientService implements IGene
new ArrayList<NamedInputStream>(uploadedFiles.size());
for (IUncheckedMultipartFile f : uploadedFiles.iterable())
{
- files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename(), f
- .getBytes()));
+ files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename()));
}
MaterialLoader loader = new MaterialLoader();
loader.load(files);
@@ -556,8 +553,7 @@ public class GenericClientService extends AbstractClientService implements IGene
new ArrayList<NamedInputStream>(uploadedFiles.size());
for (IUncheckedMultipartFile f : uploadedFiles.iterable())
{
- files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename(), f
- .getBytes()));
+ files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename()));
}
DataSetLoader loader = new DataSetLoader();
loader.load(files);
@@ -586,8 +582,7 @@ public class GenericClientService extends AbstractClientService implements IGene
new ArrayList<NamedInputStream>(uploadedFiles.size());
for (IUncheckedMultipartFile f : uploadedFiles.iterable())
{
- files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename(), f
- .getBytes()));
+ files.add(new NamedInputStream(f.getInputStream(), f.getOriginalFilename()));
}
UpdatedExperimentLoader loader = new UpdatedExperimentLoader();
loader.load(files);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/MaterialLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/MaterialLoader.java
index 613a18dd227..065cc012372 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/MaterialLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/MaterialLoader.java
@@ -10,7 +10,6 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.common.utilities.UnicodeUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.NewMaterial;
import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
@@ -41,7 +40,7 @@ public class MaterialLoader
results = new ArrayList<BatchRegistrationResult>(files.size());
for (final NamedInputStream file : files)
{
- final Reader reader = UnicodeUtils.createReader(file.getInputStream());
+ final Reader reader = file.getUnicodeReader();
final List<NewMaterial> loadedMaterials =
tabFileLoader.load(new DelegatedReader(reader, file.getOriginalFilename()));
newMaterials.addAll(loadedMaterials);
diff --git a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/UpdatedExperimentLoader.java b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/UpdatedExperimentLoader.java
index a5ef23ae77a..12d79fc40f0 100644
--- a/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/UpdatedExperimentLoader.java
+++ b/openbis/source/java/ch/systemsx/cisd/openbis/plugin/generic/client/web/server/UpdatedExperimentLoader.java
@@ -26,7 +26,6 @@ import ch.systemsx.cisd.common.parser.IParserObjectFactory;
import ch.systemsx.cisd.common.parser.IParserObjectFactoryFactory;
import ch.systemsx.cisd.common.parser.IPropertyMapper;
import ch.systemsx.cisd.common.parser.ParserException;
-import ch.systemsx.cisd.common.utilities.UnicodeUtils;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.BatchRegistrationResult;
import ch.systemsx.cisd.openbis.generic.shared.basic.dto.UpdatedBasicExperiment;
import ch.systemsx.cisd.openbis.generic.shared.parser.BisTabFileLoader;
@@ -64,7 +63,7 @@ public class UpdatedExperimentLoader
results = new ArrayList<BatchRegistrationResult>(files.size());
for (final NamedInputStream file : files)
{
- final Reader reader = UnicodeUtils.createReader(file.getInputStream());
+ final Reader reader = file.getUnicodeReader();
final List<UpdatedBasicExperiment> loadedExperiments =
tabFileLoader.load(new DelegatedReader(reader, file.getOriginalFilename()));
newExperiments.addAll(loadedExperiments);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryExtractor.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryExtractor.java
index 3001cfc0f38..a8773b455e5 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryExtractor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/LibraryExtractor.java
@@ -106,8 +106,7 @@ class LibraryExtractor
BatchSamplesOperation prepared =
SampleUploadSectionsParser.prepareSamples(typeInFile, Arrays
.asList(new NamedInputStream(new FileInputStream(platesFile), platesFile
- .getName(), null)), null, null, true,
- BatchOperationKind.REGISTRATION);
+ .getName())), null, null, true, BatchOperationKind.REGISTRATION);
List<NewSamplesWithTypes> samples = prepared.getSamples();
setUpdatableTypes(samples);
return samples;
@@ -125,7 +124,7 @@ class LibraryExtractor
{
MaterialLoader loader = new MaterialLoader();
loader.load(Arrays.asList(new NamedInputStream(new FileInputStream(genesFile), genesFile
- .getName(), null)));
+ .getName())));
return loader.getNewMaterials();
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/LibraryEntityRegistrator.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/LibraryEntityRegistrator.java
index ab65c746953..fb1face1d11 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/LibraryEntityRegistrator.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/LibraryEntityRegistrator.java
@@ -30,6 +30,7 @@ import java.util.Set;
import org.apache.commons.io.IOUtils;
import org.apache.commons.lang.StringUtils;
+import ch.systemsx.cisd.common.utilities.UnicodeUtils;
import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConstants;
/**
@@ -114,7 +115,8 @@ public class LibraryEntityRegistrator
private void writeLine(String line) throws IOException
{
- IOUtils.writeLines(Arrays.asList(line), "\n", stream);
+ IOUtils.writeLines(Arrays.asList(line), "\n", stream,
+ UnicodeUtils.DEFAULT_UNICODE_CHARSET);
}
public void close() throws IOException
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/ScreeningLibraryTransformer.java b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/ScreeningLibraryTransformer.java
index 5393aa87230..3f9e18ad982 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/ScreeningLibraryTransformer.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/plugin/screening/client/web/server/library_tools/ScreeningLibraryTransformer.java
@@ -21,12 +21,12 @@ import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStream;
-import java.nio.charset.Charset;
import com.csvreader.CsvReader;
import ch.systemsx.cisd.common.exceptions.Status;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
+import ch.systemsx.cisd.common.utilities.UnicodeUtils;
/**
* Transforms a screening library file and produces files which can be uploaded to openBIS: genes,
@@ -36,7 +36,7 @@ import ch.systemsx.cisd.common.exceptions.UserFailureException;
*/
public class ScreeningLibraryTransformer
{
- private final static char SEPARATOR = ',';
+ private final static char SEPARATOR = ','; // TODO parametrize
private static final String GENES_FILE_NAME = "genes.txt";
@@ -79,9 +79,10 @@ public class ScreeningLibraryTransformer
String plateGeometry, String groupCode, String genesFile, String oligosFile,
String platesFile)
{
+ CsvReader csvReader = null;
try
{
- CsvReader csvReader = readFile(input);
+ csvReader = readFile(input);
boolean headerPresent = csvReader.readRecord();
if (headerPresent == false)
{
@@ -99,18 +100,23 @@ public class ScreeningLibraryTransformer
registrator.register(extractor, row);
}
registrator.saveResults();
- csvReader.close();
return Status.OK;
} catch (Exception ex)
{
return Status.createError(ex.getMessage());
+ } finally
+ {
+ if (csvReader != null)
+ {
+ csvReader.close();
+ }
}
}
static CsvReader readFile(InputStream input) throws FileNotFoundException, IOException,
UserFailureException
{
- CsvReader csvReader = new CsvReader(input, Charset.defaultCharset());
+ CsvReader csvReader = new CsvReader(input, UnicodeUtils.getDefaultUnicodeCharset());
csvReader.setDelimiter(SEPARATOR);
csvReader.setSafetySwitch(false);
return csvReader;
--
GitLab