From 1a5442352497b7315738ff1f82cb356da82e9b0b Mon Sep 17 00:00:00 2001
From: tpylak <tpylak>
Date: Wed, 11 Nov 2009 13:13:17 +0000
Subject: [PATCH] LMS-1192 BatchDataSetHandler needs to support data
sets without sample
SVN: 13318
---
.../yeastx/etl/DatasetMappingResolver.java | 26 ++++++++++++-------
1 file changed, 17 insertions(+), 9 deletions(-)
diff --git a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
index 0caea447868..c542b5e385e 100644
--- a/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
+++ b/rtd_yeastx/source/java/ch/systemsx/cisd/yeastx/etl/DatasetMappingResolver.java
@@ -21,6 +21,7 @@ import java.util.Properties;
import org.apache.commons.io.FilenameUtils;
+import ch.systemsx.cisd.bds.StringUtils;
import ch.systemsx.cisd.common.collections.CollectionUtils;
import ch.systemsx.cisd.common.exceptions.EnvironmentFailureException;
import ch.systemsx.cisd.common.exceptions.UserFailureException;
@@ -214,22 +215,29 @@ class DatasetMappingResolver
{
return false;
}
- String sampleCode = tryFigureSampleCode(mapping, log);
ExperimentIdentifier experimentIdentifier = tryFigureExperimentIdentifier(mapping);
+ if (mapping.getSampleCodeOrLabel() == null && experimentIdentifier == null)
+ {
+ log.datasetMappingError(mapping, "neither sample nor experiment has been specified.");
+ return false;
+ }
+ String sampleCode = tryFigureSampleCode(mapping, log);
if (sampleCode == null)
{
- // sample can be skipped only if experiment identifier is supplied
- if (experimentIdentifier == null)
+ if (mapping.getSampleCodeOrLabel() != null)
{
- log.datasetMappingError(mapping,
- "neither sample nor experiment has been specified.");
- return false;
- } else
- {
- return experimentExists(mapping, log, experimentIdentifier);
+ return false; // error has been already reported
}
+ assert experimentIdentifier != null : "experimentIdentifier should be not null here";
+ return experimentExists(mapping, log, experimentIdentifier);
} else
{
+ if (StringUtils.isBlank(mapping.getParentDataSetCodes()) == false)
+ {
+ log.datasetMappingError(mapping,
+ "when dataset is connected to a sample it cannot have parent datasets.");
+ return false;
+ }
return sampleExistsAndBelongsToExperiment(mapping, log, sampleCode);
}
}
--
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