From 10df382516d94efd7dd7ce61024e6a8ed5238e08 Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Tue, 8 Jun 2010 08:24:15 +0000
Subject: [PATCH] LMS-1568 increase methods visibility
SVN: 16319
---
.../openbis/dss/etl/HCSDatasetUploader.java | 32 +++++++++----------
.../dss/etl/HCSImageFileExtractionResult.java | 12 +++----
.../dss/etl/PlateStorageProcessor.java | 4 +--
.../etl/ScreeningContainerDatasetInfo.java | 2 +-
4 files changed, 25 insertions(+), 25 deletions(-)
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
index 48063b947ad..ce64fe2ca03 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSDatasetUploader.java
@@ -42,7 +42,7 @@ import ch.systemsx.cisd.openbis.plugin.screening.shared.basic.dto.ScreeningConst
/**
* @author Tomasz Pylak
*/
-class HCSDatasetUploader
+public class HCSDatasetUploader
{
public static void upload(IImagingUploadDAO dao, ScreeningContainerDatasetInfo info,
List<AcquiredPlateImage> images, Set<HCSImageFileExtractionResult.Channel> channels)
@@ -132,17 +132,17 @@ class HCSDatasetUploader
throw createInvalidNewChannelException(expId, existingChannels, channelName);
}
// a channel with a specified name already exists for an experiment, its description
- // will be updated
+ // will be updated
if (existingChannel.getWavelength().equals(channelDTO.getWavelength()) == false)
- {
+ {
throw UserFailureException.fromTemplate(
- "There are already datasets registered for the experiment "
- + "which use the same channel name, but with a different wavelength! "
+ "There are already datasets registered for the experiment "
+ + "which use the same channel name, but with a different wavelength! "
+ "Channel %s, old wavelength %d, new wavelength %d.", channelName,
existingChannel.getWavelength(), channelDTO.getWavelength());
- }
- channelDTO.setId(existingChannel.getId());
- dao.updateChannel(channelDTO);
+ }
+ channelDTO.setId(existingChannel.getId());
+ dao.updateChannel(channelDTO);
return channelDTO;
}
@@ -158,18 +158,18 @@ class HCSDatasetUploader
}
private ImgChannelDTO createChannel(long expId, HCSImageFileExtractionResult.Channel channel)
- {
+ {
ImgChannelDTO channelDTO = makeChannelDTO(channel, expId);
- long channelId = dao.addChannel(channelDTO);
- channelDTO.setId(channelId);
+ long channelId = dao.addChannel(channelDTO);
+ channelDTO.setId(channelId);
return channelDTO;
}
private static ImgChannelDTO makeChannelDTO(HCSImageFileExtractionResult.Channel channel,
long expId)
{
- return ImgChannelDTO.createExperimentChannel(channel.getName(), channel.getDescription(),
- channel.getWavelength(), expId);
+ return ImgChannelDTO.createExperimentChannel(channel.getName(), channel.tryGetDescription(),
+ channel.tryGetWavelength(), expId);
}
private static class AcquiredImageInStack
@@ -330,14 +330,14 @@ class HCSDatasetUploader
ScreeningConstants.OLIGO_WELL_TYPE_CODE);
}
- String createCoordinate(ImgSpotDTO spot)
+ private static String createCoordinate(ImgSpotDTO spot)
{
return Location.tryCreateMatrixCoordinateFromLocation(new Location(spot.getColumn(), spot
.getRow()));
}
- private static Boolean[][] extractNewSpots(int rows, int columns, List<AcquiredPlateImage> images,
- List<ImgSpotDTO> existingSpots)
+ private static Boolean[][] extractNewSpots(int rows, int columns,
+ List<AcquiredPlateImage> images, List<ImgSpotDTO> existingSpots)
{
Boolean[][] spots = extractExistingSpots(rows, columns, images);
unmarkSpots(existingSpots, spots);
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
index 25d3cd0ece4..5144c71ff54 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/HCSImageFileExtractionResult.java
@@ -72,14 +72,14 @@ public final class HCSImageFileExtractionResult
private final String description;
- private final int wavelength;
+ private final Integer wavelength;
- public Channel(String name, String description, int wavelength)
+ public Channel(String name, String descriptionOrNull, Integer wavelengthOrNull)
{
assert name != null : "name is null";
this.name = name;
- this.description = description;
- this.wavelength = wavelength;
+ this.description = descriptionOrNull;
+ this.wavelength = wavelengthOrNull;
}
public String getName()
@@ -87,12 +87,12 @@ public final class HCSImageFileExtractionResult
return name;
}
- public String getDescription()
+ public String tryGetDescription()
{
return description;
}
- public int getWavelength()
+ public Integer tryGetWavelength()
{
return wavelength;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
index 1f549d6f7af..261d03e4891 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/PlateStorageProcessor.java
@@ -130,13 +130,13 @@ public final class PlateStorageProcessor extends AbstractStorageProcessor
this.currentTransaction = null;
}
- private static String[] extractChannelNames(Properties properties)
+ public static String[] extractChannelNames(Properties properties)
{
String names = PropertyUtils.getMandatoryProperty(properties, CHANNEL_NAMES);
String[] channelNames = names.split(CHANNEL_SEPARATOR);
for (int i = 0; i < channelNames.length; i++)
{
- channelNames[i] = channelNames[i].trim();
+ channelNames[i] = channelNames[i].trim().toLowerCase();
}
return channelNames;
}
diff --git a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
index 8c2de3f9987..33b0b200098 100644
--- a/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
+++ b/screening/source/java/ch/systemsx/cisd/openbis/dss/etl/ScreeningContainerDatasetInfo.java
@@ -21,7 +21,7 @@ package ch.systemsx.cisd.openbis.dss.etl;
*
* @author Tomasz Pylak
*/
-class ScreeningContainerDatasetInfo
+public class ScreeningContainerDatasetInfo
{
private String experimentPermId;
--
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